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Sample records for microsatellite polymorphism ploidy

  1. A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

    PubMed Central

    Hoffman, Joseph I.; Nichols, Hazel J.

    2011-01-01

    An important emerging application of high-throughput 454 sequencing is the isolation of molecular markers such as microsatellites from genomic DNA. However, few studies have developed microsatellites from cDNA despite the added potential for targeting candidate genes. Moreover, to develop microsatellites usually requires the evaluation of numerous primer pairs for polymorphism in the focal species. This can be time-consuming and wasteful, particularly for taxa with low genetic diversity where the majority of primers often yield monomorphic polymerase chain reaction (PCR) products. Transcriptome assemblies provide a convenient solution, functional annotation of transcripts allowing markers to be targeted towards candidate genes, while high sequence coverage in principle permits the assessment of variability in silico. Consequently, we evaluated fifty primer pairs designed to amplify microsatellites, primarily residing within transcripts related to immunity and growth, identified from an Antarctic fur seal (Arctocephalus gazella) transcriptome assembly. In silico visualization was used to classify each microsatellite as being either polymorphic or monomorphic and to quantify the number of distinct length variants, each taken to represent a different allele. The majority of loci (n = 36, 76.0%) yielded interpretable PCR products, 23 of which were polymorphic in a sample of 24 fur seal individuals. Loci that appeared variable in silico were significantly more likely to yield polymorphic PCR products, even after controlling for microsatellite length measured in silico. We also found a significant positive relationship between inferred and observed allele number. This study not only demonstrates the feasibility of generating modest panels of microsatellites targeted towards specific classes of gene, but also suggests that in silico microsatellite variability may provide a useful proxy for PCR product polymorphism. PMID:21853104

  2. Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

  3. Novel Polymorphic Multilocus Microsatellite Markers to Distinguish Candida tropicalis Isolates

    PubMed Central

    Chen, Sharon; Kong, Fanrong; Wang, He; Zhang, Li; Hou, Xin; Xu, Ying-Chun

    2016-01-01

    Candida tropicalis is an important pathogen. Here we developed and evaluated a polymorphic multilocus microsatellite scheme employing novel genetic markers for genotyping of C. tropicalis. Using 10 isolates from 10 unique (separate) patients to screen over 4000 tandem repeats from the C. tropicalis genome (strain MYA-3404), six new candidate microsatellite loci (ctm1, ctm3, ctm8, ctm18, ctm24 and ctm26) were selected according to amplification success, observed polymorphisms and stability of flanking regions by preliminary testing. Two known microsatellite loci CT14 and URA3 were also studied. The 6-locus scheme was then tested against a set of 82 different isolates from 32 patients. Microsatellite genotypes of isolates from the same patient (two to five isolates per patient) were identical. The six loci produced eight to 17 allele types and identified 11 to 24 genotypes amongst 32 patients’ isolates, achieving a discriminatory power (DP) of 0.76 to 0.97 (versus 0.78 for both CT14 and URA3 loci, respectively). Testing of a combination of only three loci, ctm1, ctm3 and ctm24, also achieved maximum typing efficiency (DP = 0.99, 29 genotypes). The microsatellite typing scheme had good correlation compared with pulsed-field gel electrophoresis, although was slightly less discriminatory. The new six-locus microsatellite typing scheme is a potentially valuable tool for genotyping and investigating microevolution of C. tropicalis. PMID:27820850

  4. Polymorphic microsatellite loci for the razor clam, Sinonovacula constricta.

    PubMed

    Ma, H-T; Jiang, H-B; Liu, X-Q; Wu, X-P; Wei, X-M

    2015-01-15

    The razor clam, Sinonovacula constricta, is an important commercial bivalve and a popular mollusca food in China. Twelve polymorphic microsatellite markers were isolated from the razor clam using a partial genomic library enriched for tandem repeat sequences of (CA)16, (GA)16. Polymorphisms of these loci were evaluated in a wild population of 30 individuals. The allele number of these polymorphic markers ranged from 5-15 per locus with an average of 9.333. Observed and expected heterozygosity values ranged from 0.192-1.000 and 0.219-0.906. Polymorphism information content ranged from 0.209-0.892 with an average of 0.704. Three loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. No significant linkage disequilibrium was detected between these loci. This set of microsatellite loci are useful for genetic studies in S. constricta.

  5. Extensive polymorphism in Cryptosporidium parvum identified by multilocus microsatellite analysis.

    PubMed

    Feng, X; Rich, S M; Akiyoshi, D; Tumwine, J K; Kekitiinwa, A; Nabukeera, N; Tzipori, S; Widmer, G

    2000-08-01

    Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.

  6. Polymorphic microsatellites for forensic identification of agarwood (Aquilaria crassna).

    PubMed

    Eurlings, Marcel C M; van Beek, Henry Heuveling; Gravendeel, Barbara

    2010-04-15

    Tropical agarwood (Aquilaria) is in danger of extinction in the wild due to illegal logging. Its resin (Gaharu) is used for the production of highly valued incense throughout Asia. We have isolated and characterized microsatellite loci of Aquilaria crassna to detect the geographic origin of agarwood for forensic applications using a modified enrichment procedure based on the capture of repetitive sequences from restricted genomic DNA. We assessed the polymorphisms of five microsatellites amplified from fresh leaves of 22 trees from seven plantations in Vietnam and Thailand and dried leaves of a herbarium specimen of one wild tree. Cross specificity of these markers was confirmed on two related Aquilaria species occurring in China and Vietnam and one microsatellite locus was successfully amplified from wood and incense samples. Four of the loci were polymorphic and the number of alleles ranged from 3 to 15. The loci characterized here can provide a starting point for forensic identification of traded material and certification of sustainably produced agarwood.

  7. Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats.

    PubMed

    Cardoso, Sara D; Gonçalves, David; Robalo, Joana I; Almada, Vitor C; Canário, Adelino V M; Oliveira, Rui F

    2013-09-01

    Transcriptome data are a good resource to develop microsatellites due to their potential in targeting candidate genes. However, developing microsatellites can be a time-consuming enterprise due to the numerous primer pairs to be tested. Therefore, the use of methodologies that make it efficient to identify polymorphic microsatellites is desirable. Here we used a 62,038 contigs transcriptome assembly, obtained from pyrosequencing a peacock blenny (Salaria pavo) multi-tissue cDNA library, to mine for microsatellites and in silico evaluation of their polymorphism. A total of 4190 microsatellites were identified in 3670 unique unigenes, and from these microsatellites, in silico polymorphism was detected in 733. We selected microsatellites based either on their in silico polymorphism and annotation results or based only on their number of repeats. Using these two approaches, 28 microsatellites were successfully amplified in twenty-six individuals, and all but 2 were found to be polymorphic, being the first genetic markers for this species. Our results showed that the strategy of selection based on number of repeats is more efficient in obtaining polymorphic microsatellites than the strategy of in silico polymorphism (allelic richness was 8.2±3.85 and 4.56±2.45 respectively). This study demonstrates that combining the knowledge of number of repeats with other predictors of variability, for example in silico microsatellite polymorphism, improves the rates of polymorphism, yielding microsatellites with higher allelic richness, and decreases the number of monomorphic microsatellites obtained.

  8. Analysis of microsatellite polymorphism in inbred knockout mice.

    PubMed

    Zuo, Baofen; Du, Xiaoyan; Zhao, Jing; Yang, Huixin; Wang, Chao; Wu, Yanhua; Lu, Jing; Wang, Ying; Chen, Zhenwen

    2012-01-01

    Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)(n) (50%, 2/4), followed by (GT)(n) (27.27%, 3/11) and (CA)(n) (23.08%, 3/13). The microsatellite CMP in (CT)(n) and (AG)(n) repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  9. Analysis of Microsatellite Polymorphism in Inbred Knockout Mice

    PubMed Central

    Zhao, Jing; Yang, Huixin; Wang, Chao; Wu, Yanhua; Lu, Jing; Wang, Ying; Chen, Zhenwen

    2012-01-01

    Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)n (50%, 2/4), followed by (GT)n (27.27%, 3/11) and (CA)n (23.08%, 3/13). The microsatellite CMP in (CT)n and (AG)n repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice. PMID:22509320

  10. Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae).

    PubMed

    Quan, Zhiwu; Pan, Lei; Ke, Weidong; Ding, Yi

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated and identified in the aquatic plant Euryale ferox Salisb. (Nymphaeaceae). This species, which belongs to basal Magnoliophyta, reproduces sexually. All of these 11 microsatellite markers yielded 25 alleles in a survey of a wild population of 34 individuals. Two or three alleles per locus were detected, with expected heterozygosity ranging from 0.056 to 0.634 and observed heterozygosity from 0.000 to 0.088. These simple sequence repeat markers will be useful for evaluating the genetic structure of the E. ferox population in the future.

  11. Polymorphic microsatellite loci for Japanese Spanish mackerel (Scomberomorus niphonius).

    PubMed

    Lin, L; Zhu, L; Liu, S-F; Tang, Q-S; Su, Y-Q; Zhuang, Z-M

    2012-05-08

    We isolated and characterized 21 polymorphic microsatellite loci in Japanese Spanish mackerel (Scomberomorus niphonius) using a (GT)(13)-enriched genomic library. Forty individuals were collected from Qingdao, China. We found 3 to 24 alleles per locus, with a mean of 8.8. The observed and expected heterozygosities ranged from 0.263 to 0.975 and from 0.385 to 0.946, with means of 0.655 and 0.685, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Two loci showed evidence for null alleles. These microsatellite markers will be useful for population genetic analysis of Japanese Spanish mackerel.

  12. Polymorphic microsatellite markers isolated from the neptune whelk Neptunea arthritica.

    PubMed

    Azuma, N; Miranda, R M; Goshima, S; Abe, S

    2009-01-01

    Eight polymorphic microsatellite DNA loci were isolated from the neptune whelk Neptunea arthritica, which is an important fishery resource in northern Japan. The number of alleles at the loci ranged from two to six, with observed and expected heterozygosities of 0.192-0.807 and 0.233-0.738, respectively. The observed variations suggest that these loci can be used as markers for population and kinship analyses in this species.

  13. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    PubMed

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  14. High polymorphism at microsatellite loci in the Chinese donkey.

    PubMed

    Zhang, R F; Xie, W M; Zhang, T; Lei, C Z

    2016-06-24

    To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

  15. Nineteen polymorphic microsatellite markers developed for Trachinotus ovatus.

    PubMed

    Xie, Z Z; Huang, M W; Xu, W; Peng, C; He, J N; Meng, Z N; Zhang, Y; Li, S S; Lin, H R

    2014-12-12

    To evaluate the population genetic diversity of the ovate pompano, we isolated and characterized 19 microsatellite markers using a (CA)13-enriched genomic library. Polymorphism was assessed in 30 individuals from a single population collected from the Daya Bay Aquaculture Center, Guangdong, China. The number of alleles per locus ranged from 2 to 18 with an average of 7.8. The observed and expected heterozygosities varied from 0.2667 to 1.000 and from 0.3960 to 0.9435, respectively. Sixteen of 19 loci conformed to Hardy-Weinberg equilibrium, and no significant linkage disequilibrium was detected between any locus pairs. Our study supplies candidate microsatellite markers that can be useful for studying the population genetic structure of ovate pompano.

  16. Development of novel polymorphic microsatellite markers in Siganus fuscescens.

    PubMed

    Mao, X Q; Li, Z B; Ning, Y F; Shangguan, J B; Yuan, Y; Huang, Y S; Li, B B

    2016-07-29

    Rabbitfish, Siganus fuscescens, is widely distributed in the Indo-Pacific regions and eastern Mediterranean. Its dwelling place includes reef flats, coral reef regions, and seagrass meadows in tropical area and reef areas or shallow waters in locations at high latitudes. In the present study, 10 new polymorphic microsatellite markers were screened from 30 wild S. fuscescens individuals, using a method of fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. The number of polymorphic alleles per locus was 3 to 5 with a mean of 4.3, while the value of polymorphic information content ranged from 0.283 to 0.680. The values of the observed and expected heterozygosities were in the range 0.3333-0.8462 and 0.3011-0.7424, respectively. Deviation from Hardy-Weinberg equilibrium was not observed in this study. These polymorphic loci are expected to be effective in evaluating the genetic diversity, population structure, and gene flow and in determining the paternity in S. fuscescens, as well as for conservation management.

  17. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    PubMed Central

    De la Rúa, Pilar; Galián, José; Serrano, José; Moritz, Robin FA

    2003-01-01

    The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees. PMID:12729553

  18. Isolation and characterization of polymorphic microsatellite loci in muskrat, Ondatra zibethicus.

    PubMed

    Laurence, S; Bewick, A J; Coltman, D W; Davis, C S; Elsasser, S C; Kidd, A G; Lesbarrères, D; Schulte-Hostedde, A I

    2009-03-01

    We describe the isolation and characterization of 12 highly polymorphic microsatellite loci for the muskrat, Ondatra zibethicus. Microsatellite markers from three other rodent species were cross-amplified in muskrat and one of them was polymorphic. We observed moderate to high levels of genetic variability in these 13 polymorphic loci (five to 22 alleles per locus) with observed heterozygosity ranging from 0.48 to 0.96. These markers will be useful for further studies on population genetic structure in muskrat and potentially in other rodent species.

  19. Polymorphic microsatellite loci for Haumania danckelmaniana and transferability to H. liebrechtsiana (Marantaceae)1

    PubMed Central

    Ley, Alexandra C.; Hardy, Olivier J.

    2016-01-01

    Premise of the study: Microsatellite markers were developed for the species Haumania danckelmaniana (Marantaceae) from central tropical Africa. Methods and Results: Microsatellite isolation was performed simultaneously on three different species of Marantaceae through a procedure that combines multiplex microsatellite enrichment and next-generation sequencing. From 80 primers selected for initial screening, 20 markers positively amplified in H. danckelmaniana, of which 10 presented unambiguous amplification products within the expected size range and eight were polymorphic with four to nine alleles per locus. Positive transferability with the related species H. liebrechtsiana was observed for the same 10 markers. Conclusions: The polymorphic microsatellite markers are suitable for studies in genetic diversity and structure, mating system, and gene flow in H. danckelmaniana and the closely related species H. liebrechtsiana. PMID:27011899

  20. Characterization of polymorphic microsatellite markers for Primula sikkimensis (Primulaceae) using a 454 sequencing approach1

    PubMed Central

    Li, Chang-Han; Liu, Yun-Jiao; Zhang, Cai-Yun; Yan, Hai-Fei; Ge, Xue-Jun; Hao, Gang

    2016-01-01

    Premise of the study: Microsatellite markers from Primula sikkimensis (Primulaceae) were developed for testing deep lineage divergence and speciation events. Methods and Results: A total of 3112 microsatellites were identified from 61,755 unique reads though 454 pyrosequencing technology. Twenty-nine microsatellite loci were selected for PCR amplification and polymorphic analyses. Among the 29 tested markers, 17 microsatellite loci were further used for genotyping in three wild P. sikkimensis populations. The number of alleles varied from one to eight, and the observed heterozygosity ranged from 0.111 to 1.000. Ten simple sequence repeat loci could be successfully cross-amplified in two Primula species. The transferability values were 76.5% in P. florindae and 58.8% in P. alpicola, respectively. Conclusions: These microsatellite markers will be valuable for testing the hypothesis of lineage divergence, genetic introgression, and cryptic speciation events between P. sikkimensis and its closely related taxa. PMID:27437171

  1. Genome polymorphisms and gene differential expression in a 'back-and-forth' ploidy-altered series of weeping lovegrass (Eragrostis curvula).

    PubMed

    Mecchia, Martín A; Ochogavía, Ana; Pablo Selva, Juan; Laspina, Natalia; Felitti, Silvina; Martelotto, Luciano G; Spangenberg, Germán; Echenique, Viviana; Pessino, Silvina C

    2007-08-01

    Molecular markers were used to analyze the genomic structure of an euploid series of Eragrostis curvula, obtained after a tetraploid dihaploidization procedure followed by chromosome re-doubling with colchicine. Considerable levels of genome polymorphisms were detected between lines. Curiously, a significant number of molecular markers showed a revertant behavior following the successive changes of ploidy, suggesting that genome alterations were specific and conferred genetic structures characteristic of a given ploidy level. Genuine reversion was confirmed by sequencing. Cluster analysis demonstrated grouping of tetraploids while the diploid was more distantly related with respect to the rest of the plants. Polymorphic revertant sequences involved mostly non-coding regions, although some of them displayed sequence homology to known genes. A revertant sequence corresponding to a P-type adenosine triphosphatase was found to be differentially represented in cDNA libraries obtained from the diploid and a colchiploid, but was not found expressed in the original tetraploid. Transcriptome profiling of inflorescence followed by real-time polymerase chain reaction validation showed 0.34% polymorphic bands between apomictic tetraploid and sexual diploid plants. Several of the polymorphic sequences corresponded to known genes. Possible correlation between the results observed here and a recently reported genome-wide non-Mendelian inheritance mechanism in Arabidopsis thaliana are discussed.

  2. Development of 14 polymorphic microsatellite loci for Ficus tikoua (Moraceae)1

    PubMed Central

    Zhang, Lu-Shui; Tan, Lu; Hu, Dai-Mei; Chen, Yan

    2016-01-01

    Premise of the study: Polymorphic microsatellite markers were developed to facilitate studies on the fine-scale population genetic structure of Ficus tikoua (Moraceae), a prostrate shrub known to have highly restricted gene flow. Methods and Results: Microsatellite primers were developed using the biotin-streptavidin capture method and scanned for polymorphism within 76 individuals sampled from three natural F. tikoua populations. Fourteen loci were shown to be polymorphic, with allele numbers ranging from three to 16. The observed and expected heterozygosity in the three populations ranged from 0 to 1 and from 0 to 0.87, respectively. Substantial divergence was found among the populations at some loci. All loci can be successfully amplified in at least eight other Ficus species, indicating good transferability within the genus. Conclusions: The 14 microsatellite loci will be a helpful tool for assessing the fine-scale genetic structure of F. tikoua. PMID:27011895

  3. Isolation and Characterization of Sixteen Polymorphic Microsatellite Loci in the Golden Apple Snail Pomacea canaliculata

    PubMed Central

    Chen, Lian; Xu, Haigen; Li, Hong; Wu, Jun; Ding, Hui; Liu, Yan

    2011-01-01

    We report the characterization of 16 polymorphic microsatellite markers in the golden apple snail, Pomacea canaliculata, a pest registered in the list of “100 of the world’s worst invasive alien species”. The fast isolation by AFLP (Amplified Fragment Length Polymorphism) of sequences containing repeats (FIASCO) method was used to isolate microsatellite loci, and polymorphism was explored with 29 individuals collected in an invasive region from China. These primers showed a number of alleles per locus ranging from three to 13. The ranges of observed and expected heterozygosity were 0.310–0.966 and 0.523–0.898, respectively. These microsatellite markers described here will be useful for population genetic studies of P. canaliculata. PMID:22016640

  4. Isolation and characterization of sixteen polymorphic microsatellite loci in the golden apple snail Pomacea canaliculata.

    PubMed

    Chen, Lian; Xu, Haigen; Li, Hong; Wu, Jun; Ding, Hui; Liu, Yan

    2011-01-01

    We report the characterization of 16 polymorphic microsatellite markers in the golden apple snail, Pomacea canaliculata, a pest registered in the list of "100 of the world's worst invasive alien species". The fast isolation by AFLP (Amplified Fragment Length Polymorphism) of sequences containing repeats (FIASCO) method was used to isolate microsatellite loci, and polymorphism was explored with 29 individuals collected in an invasive region from China. These primers showed a number of alleles per locus ranging from three to 13. The ranges of observed and expected heterozygosity were 0.310-0.966 and 0.523-0.898, respectively. These microsatellite markers described here will be useful for population genetic studies of P. canaliculata.

  5. Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans.

    PubMed

    Li, Juan; Bai, Feng-Yan

    2007-11-01

    Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.

  6. Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites.

    PubMed

    Wang, Shuang; Huang, Song; Liu, Nianjun; Chen, Liang; Oh, Cheongeun; Zhao, Hongyu

    2005-12-30

    There is currently a great interest in using single-nucleotide polymorphisms (SNPs) in genetic linkage and association studies because of the abundance of SNPs as well as the availability of high-throughput genotyping technologies. In this study, we compared the performance of whole-genome scans using SNPs with microsatellites on 143 pedigrees from the Collaborative Studies on Genetics of Alcoholism provided by Genetic Analysis Workshop 14. A total of 315 microsatellites and 10,081 SNPs from Affymetrix on 22 autosomal chromosomes were used in our analyses. We found that the results from the two scans had good overall concordance. One region on chromosome 2 and two regions on chromosome 7 showed significant linkage signals (i.e., NPL >or= 2) for alcoholism from both the SNP and microsatellite scans. The different results observed between the two scans may be explained by the difference observed in information content between the SNPs and the microsatellites.

  7. Isolation and characterization of new polymorphic microsatellite markers from the cuttlefish Sepiella maindroni (Cephalopoda; Sepiidae).

    PubMed

    Guo, B-Y; Qi, P Z; Zhu, A Y; Lv, Z M; Wang, W C; Wu, C W

    2013-07-11

    Fifteen new polymorphic microsatellite loci were developed for the cuttlefish Sepiella maindroni. In 32 individuals from a wild population of coastal Ningde, Fujian Province, China, the number of alleles at these loci varied between 2 and 12, with an average of 5.86. The mean observed and expected heterozygosities were 0.6917 and 0.5993, respectively. Among these polymorphic microsatellite loci, 4 (SM2, SM19, SM40, and SM81) significantly deviated from Hardy-Weinberg equilibrium after sequential Bonferroni's correction. All of them were in linkage equilibrium. These microsatellite loci would be useful for evaluating the effect of releasing on extant S. maindroni populations as well as for investigating genetic diversity and population structure of this species.

  8. Characterization of polymorphic microsatellite markers in Pinus armandii (Pinaceae), an endemic conifer species to China1

    PubMed Central

    Dong, Wan-Lin; Wang, Ruo-Nan; Yan, Xiao-Hao; Niu, Chuan; Gong, Lin-Lin; Li, Zhong-Hu

    2016-01-01

    Premise of the study: Pinus armandii (Pinaceae) is an important conifer tree species in central and southwestern China, and it plays a key role in the local forest ecosystems. To investigate its population genetics and design effective conservation strategies, we characterized 18 polymorphic microsatellite markers for this species. Methods and Results: Eighteen novel polymorphic and 16 monomorphic microsatellite loci of P. armandii were isolated using Illumina MiSeq technology. The number of alleles per locus ranged from two to five. The expected heterozygosity ranged from 0.061 to 0.609 with an average of 0.384, and the observed heterozygosity ranged from 0.063 to 0.947 with an average of 0.436. Seventeen loci could be successfully transferred to five related Pinus species (P. koraiensis, P. griffithii, P. sibirica, P. pumila, and P. bungeana). Conclusions: These novel microsatellites could potentially be used to investigate the population genetics of P. armandii and related species. PMID:27785387

  9. Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pityopsis graminifolia (Michx.) Small var. latifolia (Fern.) Semple is an herbaceous perennial that grows in close proximity to the federally endangered species P. ruthii (Small) Small. Twelve polymorphic microsatellite loci were identified from 87 samples of P. graminifolia var. latifolia and addit...

  10. Identification of 24 polymorphic microsatellite markers for the double-crested cormorant (Phalacrocorax auritus).

    PubMed

    Fike, Jennifer A; Devault, Travis L; Rhodes, Olin E

    2009-07-01

    Twenty-four polymorphic microsatellite markers were developed for the double-crested cormorant (Phalacrocorax auritus). The number of alleles ranged from two to 13 and observed heterozygosities ranged from 0.032 to 0.871. The use of these loci should enable researchers and biologists to learn more about the population structure and ecology of this species.

  11. Cross-Species Amplification and Polymorphism of Microsatellite Loci in the Soybean Aphid, Aphis glycines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We tested the utility of 18 previously characterized Aphis spp. microsatellite loci for polymorphism and differentiation among populations of the soybean aphid, Aphis glycines. Loci were chosen from a closely related species (Aphis gossypii) and a more distantly related species (Aphis fabae). We f...

  12. Polymorphic microsatellite markers in Anthoxanthum (Poaceae) and cross-amplification in the Eurasian complex of the genus1

    PubMed Central

    Lema-Suárez, Irene; Sahuquillo, Elvira; Marí-Mena, Neus; Pimentel, Manuel

    2016-01-01

    Premise of the study: Nonplastid microsatellite primers were developed for the first time in the Euro-Siberian complex of Anthoxanthum (Poaceae), a genus of temperate grasses in which reticulate evolution is common. Methods and Results: A microsatellite-enriched genomic DNA library allowed the detection of 500 fragments containing a microsatellite motif. Fifteen primer pairs were selected for an extended primer test. A preliminary analysis was conducted on the Eurasian diploid lineages of Anthoxanthum, with special emphasis on three populations of the Mediterranean A. aristatum–A. ovatum complex. Thirteen out of 15 markers tested were polymorphic in the complex, with successful cross-amplification in A. odoratum (93% polymorphic loci), A. amarum (73% polymorphic), A. alpinum (73% polymorphic), and A. maderense (60% polymorphic). Conclusions: These microsatellite markers will enable the analysis of evolution and phylogeography in diploid and polyploid lineages of this important genus. PMID:27785386

  13. Microsatellite polymorphism among Chrysanthemum sp. polyploids: the influence of whole genome duplication

    PubMed Central

    Wang, Haibin; Qi, Xiangyu; Gao, Ri; Wang, Jingjing; Dong, Bin; Jiang, Jiafu; Chen, Sumei; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

    2014-01-01

    Polyploidy is common among flowering plants, including the Asteraceae, a relatively recent angiosperm group. EST-SSRs were used to characterize polymorphism among 29 Chrysanthemum and Ajania spp. accessions of various ploidy levels. Most EST-SSR loci were readily transferable between the species, 29 accessions were separated into three groups in terms of the number of fragments. It inferred that the formation from tetraploid to hexaploid and from octoploid to decaploid may be a recent event, while from the diploid to the tetraploid may be an ancient one in the Chrysanthemum lineage. EST-SSR polymorphism was found and some transcripts containing an SSR were transcribed differently in the de novo autotetraploid C. nankingense and C. lavandulifolium than in their progenitor diploid. EST-SSR could provide a potential molecular basis of adaptation during evolution, while whole genome duplication has a major effect on the mutational dynamics of EST-SSR loci, which could also affect gene regulation. PMID:25339092

  14. Development of novel polymorphic microsatellite markers for the silver fox (Vulpes vulpes).

    PubMed

    Yan, S Q; Bai, C Y; Qi, S M; Li, Y M; Li, W J; Sun, J H

    2015-06-01

    The silver fox (Vulpes vulpes), a coat color variant of the red fox, is one of the most important fur-bearing animals. To date, development of microsatellite loci for the silver fox has been limited and mainly based on cross-amplification by using canine SSR primers. In this study, 28 polymorphic microsatellite markers were isolated and identified for silver fox through the construction and screening of an (AC)n-enriched library. The number of alleles per locus ranged from 2 to 8 based on 48 individuals tested. The expected and observed hetero- zygosity and polymorphism information content per locus ranged from 0.2544 to 0.859, 0.2083 to 0.7917, and 0.2181 to 0.821, respectively. The polymorphic markers presented in this study may be useful for future analysis of the genetic diversity and population structure of farmed silver fox and wild red fox.

  15. Isolation of 91 polymorphic microsatellite loci in the western Mediterranean endemic Carex helodes (Cyperaceae)1

    PubMed Central

    Arroyo, Juan M.; Escudero, Marcial; Jordano, Pedro

    2016-01-01

    Premise of the study: Microsatellite primers were developed for Carex helodes (Cyperaceae), a western Mediterranean endemic that is locally distributed in southern Portugal and southwestern Spain and rare in northern Morocco. Methods and Results: One hundred nine nuclear microsatellite markers were developed using a shotgun pyrosequencing method, resulting in 91 polymorphic and 18 monomorphic loci when tested using 19 individuals sampled from five populations from Portugal, Spain, and Morocco. Loci averaged 3.23 alleles per locus (SD = 1.15). In a single population (Cortelha population, Portugal), the 34 most polymorphic loci showed a mean observed heterozygosity of 0.357 (SD = 0.292) and mean expected heterozygosity of 0.384 (SD = 0.255). Conclusions: Next-generation sequencing allowed us to develop a high number of genetic markers with levels of polymorphism adequate to study gene flow among populations. However, when genotyping the individuals within a population, we found low levels of variation. PMID:26819859

  16. Development and characterization of polymorphic microsatellite loci for Saxifraga egregia (Saxifragaceae)1

    PubMed Central

    Zhang, Faqi; Li, Yinhu; Gao, Qingbo; Lei, Shuyun; Khan, Gulzar; Yang, Huiling; Chen, Shilong

    2015-01-01

    Premise of the study: Saxifraga egregia (Saxifragaceae) is a perennial herb that is endemic to the Qinghai–Tibet Plateau. We developed 12 polymorphic microsatellite loci for S. egregia to investigate its population genetics. Methods and Results: Forty-eight pairs of microsatellite primers (including 36 monomorphic loci) were isolated and characterized by magnetic bead enrichment. Twelve of these markers showed polymorphism, and the number of alleles per locus ranged from four to 14 across 50 individuals from three populations of S. egregia. No linkage disequilibrium was detected in any pair of loci. Conclusions: These polymorphic markers are expected to be helpful in further studies on the systematics and phylogeography of S. egregia in the Qinghai–Tibet Plateau. PMID:26312195

  17. Isolation and characterization of polymorphic microsatellite loci in the green leafhopper Empoasca vitis Goethe (Homoptera).

    PubMed

    Papura, D; Giresse, X; Chauvin, B; Caron, H; Delmotte, F; VAN Helden, M

    2009-05-01

    Eight dinucleotide microsatellite loci were isolated and characterized within the green leafhopper Empoasca vitis (Goethe) using an enrichment cloning procedure. Primers were tested on 171 individuals collected in the southwest of France from the vine plants. The identified loci were polymorphic, with allelic diversity ranging from two to 18 alleles per locus. Observed heterozygosities were from 0.021 to 0.760. These microsatellite markers should prove to be a useful tool for estimating the population genetic structure, host-plant specialization and migration capacity of this insect.

  18. Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps.

    PubMed

    Hinrichs, Anthony L; Bertelsen, Sarah; Bierut, Laura J; Dunn, Gerald; Jin, Carol H; Kauwe, John S; Suarez, Brian K

    2005-12-30

    We used the LOKI software to generate multipoint identity-by-descent matrices for a microsatellite map (with 31 markers) and two single-nucleotide polymorphism (SNP) maps to examine information content across chromosome 7 in the Collaborative Study on the Genetics of Alcoholism dataset. Despite the lower information provided by a single SNP, SNP maps overall had higher and more uniform information content across the chromosome. The Affymetrix map (578 SNPs) and the Illumina map (271 SNPs) provided almost identical information. However, increased information has a computational cost: SNP maps require 100 times as many iterations as microsatellites to produce stable estimates.

  19. Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace (Tribolodon hakonensis)

    USGS Publications Warehouse

    Koizumi, Noriyuki; Quinn, Thomas W.; Park, Myeongsoo; Fike, Jennifer A.; Nishida, Kazuya; Takemura, Takeshi; Watabe, Keiji; Mori, Atsushi

    2011-01-01

    Twenty one polymorphic microsatellite loci for the Japanese dace (Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.

  20. Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

    PubMed Central

    Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

  1. Isolation and characterization of polymorphic microsatellite markers in the endangered species Bretschneidera sinensis Hemsl.

    PubMed

    Li, M; Chen, H F; Wang, Z F; Zhang, S

    2016-08-19

    Bretschneidera sinensis is an endangered species that is mainly distributed in South China. As a tertiary relict and the single species in the Bretschneideraceae family, it has a high conservation value. To investigate the influence of human disturbance on its mating system, 63 new microsatellites were developed using restriction-site-associated DNA sequencing and their polymorphisms were tested on 30 samples from one population. Among the 63 microsatellites, the number of alleles per locus ranged from 2 to 16. The observed and expected heterozygosities ranged from 0.133 to 0.967 and from 0.127 to 0.912, respectively. These microsatellites may be used for studying the mating system of B. sinensis as well as the within-population hereditary structure.

  2. Characterization of polymorphic microsatellite markers and genetic diversity in wild bronze featherback, Notopterus notopterus (Pallas, 1769).

    PubMed

    Gupta, Arti; Lal, Kuldeep K; Punia, Peyush; Singh, Rajeev K; Mohindra, Vindhya; Sah, Rama S; Kumar, Rajesh; Luhariya, Rupesh K; Dwivedi, Arvind K; Masih, Prachi; Mishra, R M; Jena, J K

    2013-12-01

    Six polymorphic microsatellite DNA loci were identified in the primitive fish, bronze featherback, Notopterus notopterus for the first time and demonstrated significant population genetic structure. Out of the six primers, one primer (NN90) was specific to N. notopterus (microsatellite sequence within the RAG1 gene) and five primers were product of successful cross-species amplification. Sixty-four primers available from 3 fish species of order Osteoglossiformes and families Notopteridae and Osteoglossidae were tested to amplify homologous microsatellite loci in N. notopterus. Fifteen primer pairs exhibited successful cross-priming PCR product. However, polymorphism was detected only at five loci. To assess the significance of these six loci (including NN90) in population genetic study, 215 samples of N. notopterus from five rivers, viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi were analyzed. The five sample sets displayed different diversity levels and observed heterozygosity ranged from 0.6036 to 0.7373. Significant genotype heterogeneity (P < 0.0001) and high FST (0.2205) over all loci indicated that the samples are not drawn from the same genepool. The identified microsatellite loci are promising for use in fine-scale population structure analysis of N. notopterus.

  3. Development of 23 polymorphic microsatellite loci in invasive silver wattle, Acacia dealbata (Fabaceae)1

    PubMed Central

    Guillemaud, Thomas; Broadhurst, Linda; Legoff, Isabelle; Henery, Martin; Blin, Aurélie; Ducatillion, Catherine; Ferrando, Nathalie; Malausa, Thibaut

    2015-01-01

    Premise of the study: Microsatellite markers were developed for silver wattle, Acacia dealbata (Fabaceae), which is both an ornamental and an invasive weed species. It is native to southeastern Australia and invasive in Europe, Africa, Asia, and the Americas. Methods and Results: The pyrosequencing of a microsatellite-enriched genomic DNA library of A. dealbata produced 33,290 sequences and allowed the isolation of 201 loci with a minimum of seven repeats of microsatellite motifs. Amplification tests led to the setup of two multiplex PCR mixes allowing the amplification of 21 loci. The polymorphism of these markers was evaluated on a sample of 32 individuals collected in southeastern Australia. The number of alleles and the expected heterozygosity varied between two and 11, and between 0.11 and 0.88, respectively. Conclusions: The level of polymorphism of this set of 23 microsatellites is large enough to provide valuable information on the genetic structure and the invasion history of A. dealbata. PMID:25995979

  4. Eleven Novel Polymorphic Microsatellite Loci for Oval Squid Sepioteuthis Lessoniana (Shiro-Ika Type)

    PubMed Central

    Tomano, Satoshi; Ahmad-Syazni, Kamarudin; Ueta, Yukio; Ohara, Kenichi; Umino, Tetsuya

    2013-01-01

    The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future. PMID:24108369

  5. Isolation and characterization of polymorphic microsatellite loci for Pachycrepoideus vindemmiae (Rondani) (Hymenoptera: Pteromalidae).

    PubMed

    Chen, W; Fang, L; Liu, J L; He, Z; Hu, H Y

    2015-03-13

    The parasitoid wasp Pachycrepoideus vindemmiae (Rondani) is a common pupal parasitoid of many fly pests that is distributed worldwide. This organism can be used for biological control in orchards or livestock farms. Identifying polymorphic microsatellite loci would be useful for analyzing the population genetic structure of the parasitoid. In the current study, based on a modified biotin-capture method, 10 polymorphic microsatellite loci were isolated and characterized for the insect, 7 of which did not deviate from Hardy-Weinberg equilibrium. The allelic number per locus varied from 3-7 (N = 30). The expected and observed heterozygosities of 10 loci ranged from 0.369-0.775 and from 0.300-0.867, respectively.

  6. Development and characterisation of nine polymorphic microsatellite markers for Tephrosia calophylla Bedd. (Fabaceae).

    PubMed

    Parine, Narasimha Reddy; Lakshmi, P; Kumar, Devinder; Shaik, Jilani P; Alanazi, Mohammed; Pathan, Akbar Ali Khan

    2015-03-01

    Tephrosia calophylla Bedd. (Fabaceae) is an endangered tropical plant endemic to southwestern Ghats, India. The objective of this study was to contribute to the characterisation of the diversity of this rare species, which is necessary for its future conservation. Accordingly, microsatellite markers were designed, and their ability to detect polymorphisms was determined. Nine microsatellite markers were developed using genomic libraries, and all of the markers were successfully amplified in 42 individuals. Three to nine alleles per locus were observed, and the heterozygosity of the loci ranged from 0.381 to 0.905. The nine newly developed polymorphic markers recognise a sufficient number of varying loci to perform further studies on the conservation and breeding of this medicinal cultivar.

  7. Development and characterisation of nine polymorphic microsatellite markers for Tephrosia calophylla Bedd. (Fabaceae)

    PubMed Central

    Parine, Narasimha Reddy; Lakshmi, P.; Kumar, Devinder; Shaik, Jilani P.; Alanazi, Mohammed; Pathan, Akbar Ali Khan

    2014-01-01

    Tephrosia calophylla Bedd. (Fabaceae) is an endangered tropical plant endemic to southwestern Ghats, India. The objective of this study was to contribute to the characterisation of the diversity of this rare species, which is necessary for its future conservation. Accordingly, microsatellite markers were designed, and their ability to detect polymorphisms was determined. Nine microsatellite markers were developed using genomic libraries, and all of the markers were successfully amplified in 42 individuals. Three to nine alleles per locus were observed, and the heterozygosity of the loci ranged from 0.381 to 0.905. The nine newly developed polymorphic markers recognise a sufficient number of varying loci to perform further studies on the conservation and breeding of this medicinal cultivar. PMID:25737647

  8. Development of 12 polymorphic microsatellite loci for the endangered Seychelles palm Lodoicea maldivica (Arecaceae)1

    PubMed Central

    Morgan, Emma J.; Määttänen, Kirsti; Kaiser-Bunbury, Christopher N.; Buser, Andres; Fleischer-Dogley, Frauke; Kettle, Chris J.

    2016-01-01

    Premise of the study: The evolutionarily and ecologically distinct coco de mer palm Lodoicea maldivica (Arecaceae) is endemic to two islands in the Seychelles. Before colonization of the islands by man, the endangered palm formed large monodominant stands, but its natural range is now restricted to four main populations and several patches of isolated individuals. Microsatellite markers were designed to investigate the genetic structure of the remaining natural populations of L. maldivica. Methods and Results: We developed 12 polymorphic and three monomorphic microsatellite markers for this species, with a mean number of alleles per locus of 13.2 (range 5–21) and expected heterozygosity values ranging from 0.31–0.91 for the polymorphic loci. Conclusions: These markers enable us to study the patterns of genetic diversity, contemporary seed dispersal, and the fine-scale spatial genetic structure of this important conservation flagship species. PMID:27144106

  9. Isolation and Characterization of Polymorphic Microsatellite Markers from the Chinese Medicinal Herb Atractylodes macrocephala (Asteraceae)

    PubMed Central

    Zheng, Li; Shao, Zhong-Da; Wang, Zong-Chao; Fu, Cheng-Xin

    2012-01-01

    Atractylodes macrocephala Koidz. (Asteraceae) is an economically important Chinese medicinal herb. In this study, 15 polymorphic microsatellite markers were developed from A. macrocephala using the compound microsatellite marker technique. Levels of polymorphism within the 15 markers were assessed using 83 individuals from two wild and two cultivated populations in China. The number of alleles per locus ranged from 2 to 20, with an average of 9.9 alleles. Observed and expected heterozygosities ranged from 0.083 to 1.000 and from 0.097 to 0.938, respectively. These markers will be valuable for germplasm classification and identification, as well as for assessing the genetic diversity and spatial genetic structure among wild and cultivated populations of A. macrocephala. PMID:23443109

  10. Polymorphic microsatellite markers for the striped skunk, Mephitis mephitis, and other mephitids.

    PubMed

    Dragoo, Jerry W; Coan, Kathryn E; Moore, Kristin A; Henke, Scott E; Fleischer, Robert C; Wisely, Samantha M

    2009-01-01

    We report 10 polymorphic microsatellite loci primers developed for striped skunks (Mephitis mephitis), a widespread mesocarnivore in North America. Numbers of alleles in these loci ranged from seven to 14 and the observed heterozygosity ranged from 0.76 to 1.0. These primers will be useful for studying population dynamics of skunks where rabies is endemic and will be useful to estimate genetic relatedness among females sharing winter dens. Most of these primers amplify across species within the Mephitidae.

  11. Development of polymorphic microsatellite markers for Dioscorea zingiberensis and cross-amplification in other Dioscorea species.

    PubMed

    Yan, Q-Q; Sun, X-Q; Guo, J-L; Hang, Y-Y; Li, M-M

    2013-09-19

    Dioscorea zingiberensis C.H. Wright (Dioscoreaceae) is an endemic species in central and southwestern China. In order to study the genetic diversity and population structure of this species, 19 novel polymorphic microsatellite loci were developed using a dual-suppression PCR technique. The number of alleles per locus ranged from 3 to 21, with an average of 9.53. All the markers showed high transferability in cross-species amplification in other species of sect. Stenophora.

  12. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals.

    PubMed

    Vukosavljev, M; Esselink, G D; van 't Westende, W P C; Cox, P; Visser, R G F; Arens, P; Smulders, M J M

    2015-01-01

    The first hurdle in developing microsatellite markers, cloning, has been overcome by next-generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6-20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.

  13. Polymorphic microsatellite loci identified through development and cross-species amplification within shorebirds

    USGS Publications Warehouse

    Williams, I.; Guzzetti, B.M.; Gust, Judy R.; Sage, G.K.; Gill, R.E.; Tibbitts, T.L.; Sonsthagen, S.A.; Talbot, S.L.

    2012-01-01

    We developed microsatellite loci for demographic assessments of shorebirds, a group with limited markers. First, we isolated five dinucleotide repeat microsatellite loci from the Black Oystercatcher (Haematopodidae: Haematopus bachmani), and three from the Bristle-thighed Curlew (Scolopacidae: Numenius tahitiensis); both species are of conservation concern. All eight loci were polymorphic in their respective target species. Hbaμ loci were characterized by two to three alleles with observed heterozygosity ranging from 0.07 to 0.33, and two to nine alleles were detected for Nut loci with observed heterozygosity ranging from 0.08 to 0.72. No linkage disequilibrium or departures from Hardy–Weinberg equilibrium were observed. The eight loci were also tested for cross-species amplification in 12 other species within Charadriidae and Scolopacidae, and the results demonstrated transferability across several genera. We further tested all 14 species at 12 additional microsatellite markers developed for other shorebirds: Dunlin (Calidris alpina; four loci) and Ruff (Philomachus pugnax; eight loci). Two markers (Hbaμ4 and Ruff6) were polymorphic in 13 species, while two (Calp6 and Ruff9) were monomorphic. The remaining eight markers revealed polymorphism in one to nine species each. Our results provide further evidence that locus Ruff10 is sex-linked, contrary to the initial description. These markers can be used to enhance our understanding of shorebird biology by, for example, helping to determine migratory connectivity among breeding and wintering populations and detecting relatedness among individuals.

  14. VNTR and microsatellite polymorphisms within the subtelomeric region of 7q

    SciTech Connect

    Helms, C.; Donis-Keller, H. ); Hing, A.V.

    1993-08-01

    The molecular basis of a highly polymorphic RFLP marker, HTY146c3 (D7S591), within the subtelomeric region of human chromosome 7q was determined by restriction-fragment and DNA sequence analysis. Two polymorphic systems were found - a simple base-substitution polymorphism and a GC-rich VNTR element with a core structure of C[sub 3]AG[sub 2]C[sub 2]. In addition, a compound-imperfect CA dinucleotide-repeat element was identified approximately 10-20 kb from the telomeric sequence repeat (T[sub 2]AG[sub 3]), demonstrating that microsatellites can extend essentially to the ends of human chromosomes. The microsatellite marker, sAVH-6 (D7S594), is highly polymorphic, with 10 alleles and an observed heterozygosity of 84% found with the CEPH (Centre d'Etude du Polymorphisme Humain) reference pedigree collection. In combination with the RFLPs, the informativeness of the markers contained within 240 kb at the telomere approaches 100%. A unique genetic and physical STS marker, sAVH-6, defines the endpoint of the long arm of human chromosome 7. 33 refs., 4 figs., 2 tabs.

  15. Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite

    PubMed Central

    Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A.; Upcroft, Jacqui; Sullivan, Steven A.; Tachezy, Jan; Carlton, Jane M.

    2010-01-01

    Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates. PMID:20813140

  16. Genetic polymorphism of Hucul horse population based on 17 microsatellite loci.

    PubMed

    Fornal, Agnieszka; Radko, Anna; Piestrzyńska-Kajtoch, Agata

    2013-01-01

    Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyped and mean number of alleles per locus was estimated (7.00). Means of observed (Ho) and expected (He) heterozygosity were calculated 0.7288 and 0.7027, respectively. The observed heterozygosity was similar to the results of research on Hucul horse population in another area of Carpathians Mountains. The average polymorphism information content (PIC) for analyses of seventeen microsatellite markers indicates the usefulness of this set of markers for Hucul horse parentage testing.

  17. Microsatellite DNA polymorphisms and the relation with body weight in sea cucumber Apostichopus japonicus

    NASA Astrophysics Data System (ADS)

    Wang, Xiuli; Shan, Xue; Qiu, Xuemei; Meng, Xiangying; Chang, Yaqing

    2009-05-01

    The relationship between microsatellite polymorphism and body weight of captive bred Chinese sea cucumber Apostichopus japonicus was investigated in two local populations in Dalian. Among ten loci discovered, nine show changes except for AJ07 loci. Seven loci were found highly polymorphic in both populations. For each locus in two populations, the average number of alleles is 6.428 6 and 6.285 7, the average observed heterozygosity at 0.225 7 and 0.245 9, the expected heterozygosity at 0.776 8 and 0.748 8, the polymorphism information content (PIC) at 0.709 2 and 0.674 6, respectively. Further analysis show significant correlation between A. japonicus body weight and occurrence markers AJ02 and AJ04. The findings of the relation may be helpful for molecular breeding, as well as the marker-assisted selection of sea cucumbers.

  18. Isolation and characterization of polymorphic microsatellite loci in Spondias radlkoferi (Anacardiaceae)1

    PubMed Central

    Aguilar-Barajas, Esther; Sork, Victoria L.; González-Zamora, Arturo; Rocha-Ramírez, Víctor; Arroyo-Rodríguez, Víctor; Oyama, Ken

    2014-01-01

    • Premise of the study: Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. • Methods and Results: Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. • Conclusions: These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi) on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest. PMID:25383270

  19. Isolation and Characterization of 11 Polymorphic Microsatellite Markers Developed for Orthops palus (Heteroptera: Miridae)

    PubMed Central

    Atiama, M.; Delatte, H.; Deguine, J.-P.

    2016-01-01

    Miridae (Hemiptera: Heteroptera: Cimicomorpha), or plant bugs, are one of the most diverse and species-rich families of insects. Most of them are phytophagous, but some are insect predators and used for biocontrol. Among this family, the mango bug, Orthops palus (Taylor 1947), is one of the most important pest of mango in Reunion Island. We developed 11 polymorphic microsatellite loci to study the population genetics of this pest species. The microsatellite markers were characterized by genotyping 78 field-collected insects sampled at different localities in Reunion Island. The number of alleles per locus ranged from 1 to 13 and heterozygosity levels ranged between 0.40 and 0.94. Several loci were not at Hardy–Weinberg equilibrium for the tested populations. These markers are the first to be developed for a species of the genus Orthops. PMID:26922804

  20. Isolation and characterization of nine polymorphic microsatellite loci of the kelp greenling, Hexagrammos decagrammus, a temperate reef fish.

    PubMed

    Freiwald, Jan; Stewart, Nathan L; Yates, Devona C; Bernardi, Giacomo

    2009-03-01

    Nine polymorphic microsatellite loci were developed and characterized for the temperate reef fish species, Hexagrammos decagrammus (kelp greenling). The number of alleles varied from three to 22 in a sample of 22 individuals from one population. Expected heterozygosities ranged from 0.354 to 0.979. These microsatellites allow us to investigate reproductive success of individuals, alternative mating strategies as well as population structure and metapopulation dynamics of this species.

  1. Development and characterization of eight polymorphic microsatellite loci from Pistacia lentiscus L. (Anacardiaceae).

    PubMed

    Albaladejo, Rafael G; Sebastiani, F; Aparicio, A; Buonamici, A; González-Martínez, S C; Vendramin, G G

    2008-07-01

    We have developed a set of eight polymorphic nuclear microsatellite markers for the Mediterranean shrub Pistacia lentiscus by means of an enriched library method. Characterization for the eight loci was carried out on 42 individuals from two populations sampled in southern Spain. The overall number of alleles detected was 59, ranging from three to 13 per locus. Expected heterozygosity per locus and population ranged from 0.139 to 0.895. Two loci albeit only in one population (Seville) departed significantly from Hardy-Weinberg equilibrium expectations and no linkage disequilibrium between pairs of loci was detected. These markers will be used in studies of gene flow across a fragmented landscape.

  2. Ten polymorphic microsatellite loci for Allobates femoralis, an Amazonian dendrobatoid frog.

    PubMed

    Jehle, R; Gasser, H; Pfunder, M; Amézquita, A; Lima, A P; Hödl, W

    2008-11-01

    Within the anuran amphibians, dendrobatoids (poison-arrow frogs) are renowned for their parental care, but the lack of highly variable DNA markers so far precluded precise and comprehensive measurements of their genetic mating system. Here we present 10 polymorphic microsatellites for Allobates femoralis, a widespread dendrobatoid from the Amazon basin. In 24 field-collected individuals, we found between seven and 15 alleles per locus, without deviations from Hardy-Weinberg equilibrium or linkage disequilibrium. The loci will be employed to quantify reproductive success in view of male territoriality and female mate choice, as well as to determine the fine-scale genetic structure of local populations.

  3. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

    USGS Publications Warehouse

    Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

    2007-01-01

    Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

  4. Isolation, characterization and PCR multiplexing of polymorphic microsatellite markers in the edible dormouse, Glis glis.

    PubMed

    Hürner, H; Martin, J F; Ribas, A; Arrizabalaga, A; Michaux, J R

    2009-05-01

    We isolated and characterized 10 dinucleotide microsatellite loci in the edible dormouse, Glis glis (Linnaeus). Four multiplex panels were developed. Loci were amplified in samples from two geographically distant populations (Torgny in Belgium and Montseny in Spain). All loci were polymorphic in Spain but four were monomorphic in Belgium. Individuals from Belgium and Spain exhibited an average allelic diversity of 1.9 and 3.3 and an observed heterozygosity ranging from 0.08 to 0.47 and from 0.04 to 0.72, respectively.

  5. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata

    PubMed Central

    Jamsari, Amirul Firdaus Jamaluddin; Min-Pau, Tan; Siti-Azizah, Mohd Nor

    2011-01-01

    Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata. PMID:21734840

  6. Development of polymorphic microsatellite markers issued from pyrosequencing technology for the medicinal mushroom Agaricus subrufescens.

    PubMed

    Foulongne-Oriol, Marie; Spataro, Cathy; Moinard, Magalie; Cabannes, Delphine; Callac, Philippe; Savoie, Jean-Michel

    2012-09-01

    The recently described procedure of microsatellite-enriched library pyrosequencing was used to isolate microsatellite loci in the gourmet and medicinal mushroom Agaricus subrufescens. Three hundred and five candidate loci containing at least one simple sequence repeats (SSR) locus and for which primers design was successful, were obtained. From a subset of 95 loci, 35 operational and polymorphic SSR markers were developed and characterized on a sample of 14 A. subrufescens genotypes from diverse origins. These SubSSR markers each displayed from two to 10 alleles with an average of 4.66 alleles per locus. The observed heterozygosity ranged from 0 to 0.71. Several multiplex combinations can be set up, making it possible to genotype up to six markers easily and simultaneously. Cross-amplification in some closely congeneric species was successful for a subset of loci. The 35 microsatellite markers developed here provide a highly valuable molecular tool to study genetic diversity and reproductive biology of A. subrufescens.

  7. Development of 15 polymorphic microsatellite markers for Ficus virens (Moraceae)1

    PubMed Central

    Fu, Rong-Hua; Li, Yun-Xiang; Liu, Mei; Quan, Qiu-Mei

    2017-01-01

    Premise of the study: Ficus virens (Moraceae) is distributed widely in South and Southeast Asia, Melanesia, and northern Australia, and it is also cultivated outside its original northern range limit in southwestern China. Therefore, the species is well suited to explore the mechanism of range limits of Ficus species. However, little is known about its genetic background. Methods and Results: Fifteen polymorphic microsatellite markers were developed using the biotin-streptavidin capture method. Polymorphism was tested in 85 F. virens individuals sampled from three populations. The number of alleles ranged from three to 17. The observed and expected heterozygosity of each population varied from 0.0667 to 0.9286 and 0.0650 to 0.8890, respectively. Cross-species amplification was also carried out in eight other Ficus species. Conclusions: These 15 markers will be valuable for studying the genetic variation and population structure of F. virens and related Ficus species. PMID:28090407

  8. Microsatellite polymorphisms in cassava landraces from the Cerrado biome, Mato Grosso do sul, Brazil.

    PubMed

    Siqueira, M V B M; Pinheiro, T T; Borges, A; Valle, T L; Zatarim, M; Veasey, E A

    2010-10-01

    Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region's high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.

  9. Polymorphic microsatellites in nēnē, the endangered Hawaiian goose (Branta sandvicensis).

    PubMed

    Veillet, Anne; Shrestha, Rajesh; Price, Donald K

    2008-09-01

    The nēnē (Branta sandvicensis) is an endangered Hawaiian goose endemic to the Hawaiian Islands. The nēnē nearly went extinct in the mid-19.00s and the majority of the approximately 1300 individuals currently in Hawai'i are descendants from less than 30 birds. The low adult breeding success and juvenile survival is likely due, in part, to inbreeding depression in wild individuals. Thirty-eight microsatellite primer sets developed in nēnē, Canada goose, and waterfowl species provided 8 polymorphic loci. Four of these polymorphic loci exhibited only two alleles, which is likely a reflection of the high inbreeding in this species.

  10. [Genetic analysis of microsatellite polymorphism in the Elliot's Pheasant (Syrmaticus ellioti) in China].

    PubMed

    Lin, Fang-Jun; Jiang, Ping-Ping; Ding, Ping

    2010-10-01

    In this study, we reported the population genetic analyses in the Elliot's Pheasant(Syrnaticus ellioti) using seven polymorphism microsatellite loci based on 105 individuals from 4 geographical populations. Departures from Hardy-Weinberg equilibrium were found in four geographical populations. The average number of alleles was 8.86, with a total of 62 alleles across 7 loci; observed heterozygosity (HO) was generally low and the average number was 0.504. For the seven microsatellite loci, the polymorphism information content ranged from 0.549 to 0.860, with an average number 0.712. Population bottlenecks of the four geographical populations were tested by infinite allele mutation model, step-wise mutation model and two-phase mutation model, which found that each population had experienced bottleneck effect during the recent period. Fst analysis across all geographical populations indicated that the genetic differentiaton between the Guizhou geographical population and the Hunan geographical population was highly significant (P<0.001), a finding supported by the far genetic relationship showed by the neighbor-joining tree of four geographical populations based on Nei's unbiased genetic distances. Using hierarchical analysis of molecular variance (Guizhou geographical population relative to all others pooled), we found a low level of the genetic variation among geographical populations and that between groups. However, differences among populations relative to the total sample explained most of the genetic variance (92.84%), which was significant.

  11. Typing Candida Species Using Microsatellite Length Polymorphism and Multilocus Sequence Typing.

    PubMed

    Garcia-Hermoso, Dea; Desnos-Ollivier, Marie; Bretagne, Stéphane

    2016-01-01

    To gain more insight into the epidemiological relationships between isolates of Candida spp. obtained from various origins, several molecular typing techniques have been developed. Two methods have emerged in the 2000s as soon as enough knowledge of the Candida spp. genomes was available to choose adequate loci and primers, namely microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST). To contrast with previous PCR-based methods, specific amplifications with stringent conditions easily reproducible are the basis of MLP and MLST. MLST relies on Sanger sequencing to detect single-nucleotide polymorphisms within housekeeping genes. MLP needs a first in silico step to select tandemly repeated stretches of two to five nucleotides. One of the two primers used to amplify a microsatellite locus is labeled and fragment sizing is automatically performed using high-resolution electrophoresis platforms. MLST provides results easily comparable between laboratories and active MLST schemes are publicly available for the main Candida species. For comparative studies, MLP needs standards to compensate for the electrophoretic variations depending on the platforms used. Both methods can help us gain insight into the genetic relatedness of fungal isolates, both with advantages and drawbacks, and the choice of one method rather than the other depends on the task in question.

  12. Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism.

    PubMed Central

    Bergström, T F; Engkvist, H; Erlandsson, R; Josefsson, A; Mack, S J; Erlich, H A; Gyllensten, U

    1999-01-01

    We analyzed the origin of allelic diversity at the class II HLA-DRB1 locus, using a complex microsatellite located in intron 2, close to the polymorphic second exon. A phylogenetic analysis of human, gorilla, and chimpanzee DRB1 sequences indicated that the structure of the microsatellite has evolved, primarily by point mutations, from a putative ancestral (GT)x(GA)y-complex-dinucleotide repeat. In all contemporary DRB1 allelic lineages, with the exception of the human *04 and the gorilla *08 lineages, the (GA)y repeat is interrupted, often by a G-->C substitution. In general, the length of the 3' (GA)y repeat correlates with the allelic lineage and thus evolves more slowly than a middle (GA)z repeat, whose length correlates with specific alleles within the lineage. Comparison of the microsatellite sequence from 30 human DRB1 alleles showed the longer 5' (GT)x to be more variable than the shorter middle (GA)z and 3' (GA)y repeats. Analysis of multiple samples with the same exon sequence, derived from different continents, showed that the 5' (GT)x repeat evolves more rapidly than the middle (GA)z and the 3' (GA)y repeats, which is consistent with findings of a higher mutation rate for longer tracts. The microsatellite-repeat-length variation was used to trace the origin of new DRB1 alleles, such as the new *08 alleles found in the Cayapa people of Ecuador and the Ticuna people of Brazil. PMID:10330359

  13. Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers.

    PubMed

    Ben Tamarzizt, H; Ben Mustapha, S; Baraket, G; Abdallah, D; Salhi-Hannachi, A

    2015-03-20

    The usefulness of random amplified microsatellite polymorphism markers to study the genetic diversity and relationships among cultivars belonging to Prunus salicina and P. domestica and their wild relatives (P. insititia and P. spinosa) was investigated. A total of 226 of 234 bands were polymorphic (96.58%). The 226 random amplified microsatellite polymorphism markers were screened using 15 random amplified polymorphic DNA and inter-simple sequence repeat primers combinations for 54 Tunisian plum accessions. The percentage of polymorphic bands (96.58%), the resolving power of primers values (135.70), and the polymorphic information content demonstrated the efficiency of the primers used in this study. The genetic distances between accessions ranged from 0.18 to 0.79 with a mean of 0.24, suggesting a high level of genetic diversity at the intra- and interspecific levels. The unweighted pair group with arithmetic mean dendrogram and principal component analysis discriminated cultivars efficiently and illustrated relationships and divergence between spontaneous, locally cultivated, and introduced plum types. These procedures showed continuous variation that occurs independently of the status of the species and geographical origin of the plums. In this study, random amplified microsatellite polymorphism was found to be as a reliable molecular marker for fingerprinting and for examining the diversity study of the plum and its relatives.

  14. Clinical and Biochemical Function of Polymorphic NR0B1 GGAA-Microsatellites in Ewing Sarcoma: A Report from the Children's Oncology Group

    PubMed Central

    Monument, Michael J.; Johnson, Kirsten M.; McIlvaine, Elizabeth; Abegglen, Lisa; Watkins, W. Scott; Jorde, Lynn B.; Womer, Richard B.; Beeler, Natalie; Monovich, Laura; Lawlor, Elizabeth R.; Bridge, Julia A.; Schiffman, Joshua D.; Krailo, Mark D.; Randall, R. Lor; Lessnick, Stephen L.

    2014-01-01

    Background The genetics involved in Ewing sarcoma susceptibility and prognosis are poorly understood. EWS/FLI and related EWS/ETS chimeras upregulate numerous gene targets via promoter-based GGAA-microsatellite response elements. These microsatellites are highly polymorphic in humans, and preliminary evidence suggests EWS/FLI-mediated gene expression is highly dependent on the number of GGAA motifs within the microsatellite. Objectives Here we sought to examine the polymorphic spectrum of a GGAA-microsatellite within the NR0B1 promoter (a critical EWS/FLI target) in primary Ewing sarcoma tumors, and characterize how this polymorphism influences gene expression and clinical outcomes. Results A complex, bimodal pattern of EWS/FLI-mediated gene expression was observed across a wide range of GGAA motifs, with maximal expression observed in constructs containing 20–26 GGAA motifs. Relative to white European and African controls, the NR0B1 GGAA-microsatellite in tumor cells demonstrated a strong bias for haplotypes containing 21–25 GGAA motifs suggesting a relationship between microsatellite function and disease susceptibility. This selection bias was not a product of microsatellite instability in tumor samples, nor was there a correlation between NR0B1 GGAA-microsatellite polymorphisms and survival outcomes. Conclusions These data suggest that GGAA-microsatellite polymorphisms observed in human populations modulate EWS/FLI-mediated gene expression and may influence disease susceptibility in Ewing sarcoma. PMID:25093581

  15. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    PubMed

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  16. Changing Ploidy as a Strategy: The Irish Potato Famine Pathogen Shifts Ploidy in Relation to Its Sexuality.

    PubMed

    Li, Ying; Shen, He; Zhou, Qian; Qian, Kun; van der Lee, Theo; Huang, Sanwen

    2017-01-01

    The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high potential to adapt to various environments and great risk to break disease resistance genes in potato. As are other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of single nucleotide polymorphisms, nuclear DNA quantification, and microscopic counting of chromosome numbers, we assessed the ploidy level of a comprehensive selection of isolates. All progenies from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level may be a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.

  17. Microsatellite Markers of Willow Species and Characterization of 11 Polymorphic Microsatellites for Salix eriocephala (Salicaceae), a Potential Native Species for Biomass Production in Canada.

    PubMed

    Lauron-Moreau, Aurélien; Pitre, Frédéric E; Brouillet, Luc; Labrecque, Michel

    2013-03-27

    Biomass produced from dedicated plantations constitutes a source of renewable energy and is expected to play an important role in several countries in the coming decades. The cultivation of woody crops such as willows therefore raises several environmental issues. In North America, several native willows are potentially interesting for biomass producers. Willow trees are diverse but few species used for environmental applications have been the object of molecular genetic studies. Based on the sequenced poplar genome, 24 microsatellite markers were assayed on five native North American willow species: Salix amygdaloides, S. discolor, S. eriocephala, S. interior and S. nigra. Polymorphic microsatellite markers were used to characterize the allele data on the shrub Salix eriocephala, a North American species with economic potential. Eleven markers amplified and confirmed the potential of this species. Analysis of samples from six populations in eastern Canada showed that all markers were variable as well as polymorphic in at least one population. The number of alleles per locus ranged from 1 to 9 (mean 2.95) and showed that these microsatellite markers can be used to assess genetic diversity of North American willow species.

  18. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids.

    PubMed

    Boto, Luis; Cunha, Carina; Doadrio, Ignacio

    2011-07-01

    A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose..

  19. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids

    PubMed Central

    Boto, Luis; Cunha, Carina; Doadrio, Ignacio

    2011-01-01

    A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.. PMID:21931529

  20. Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers.

    PubMed

    Berber, N; Gaouar, S; Leroy, G; Kdidi, S; Tabet Aouel, N; Saïdi Mehtar, N

    2014-10-01

    In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab-Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab-Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (FST ). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab-Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population.

  1. Outcrossing and paternity analysis of Pinus densiflora (Japanese red pine) by microsatellite polymorphism.

    PubMed

    Lian, C; Miwa, M; Hogetsu, T

    2001-07-01

    This study employed microsatellite loci to analyse outcrossing rate and pollen dispersal in Japanese red pine (Pinus densiflora) in an isolated stand. The average offspring outcrossing rate for 29 cones was 0.955. Significant differences in outcrossing rates between offspring groups on individual branches that extended in different directions at different heights were not detected. Male parents of 874 offspring collected from the maternal tree were assessed by exclusion using polymorphisms at three microsatellite loci. Paternity analysis indicated that at least 31% of the offspring were fertilized by pollen from trees outside the stand. The average distance of pollen migration within the study stand was 68 m, with a maximum value of 325 m. There was excess mating with nearby P. densiflora trees, of which only a few were predominant pollen donors. In addition, a weakly directional bias in P. densiflora pollination was also detected in the study stand, suggesting that female strobili on a branch of the maternal tree were more easily fertilized by pollen from trees in that direction.

  2. Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta).

    PubMed

    Mace, Emma S; Godwin, Ian D

    2002-10-01

    Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.

  3. Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae).

    PubMed

    Landínez-García, Ricardo M; Márquez, Edna J

    2016-01-01

    The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.

  4. Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae)

    PubMed Central

    Landínez-García, Ricardo M.

    2016-01-01

    The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae. PMID:27635363

  5. Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)

    USGS Publications Warehouse

    Campbell, Matthew A.; Sage, George K.; DeWilde, Rachel L.; López, J. Andres; Talbot, Sandra L.

    2014-01-01

    Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We developed sixteen polymorphic microsatellites from the Alaska blackfish (Dallia pectoralis) to study genetic diversity in Dallia. Genotypes from two populations, Denali (n = 31) and Bethel (n = 35), demonstrated the usefulness of the loci for population-level investigation. Observed and expected heterozygosity averaged 18.6 and 19.8 % in Denali and 61.1 and 63.7 % in Bethel. Number of alleles at each locus averaged 3.50 in Denali and 9.63 in Bethel. The observed signature of variability and structuring between populations is consistent with mitochondrial data.

  6. [Polymorphism of microsatellite loci in cultivars and species of pear (Pyrus L.)].

    PubMed

    Iakovin, N A; Fesenko, I A; Isachkin, A V; Karlov, G I

    2011-05-01

    Using five SSR markers, polymorphism ofmicrosatellite loci was examined in 46 cultivars and five species of pear (Pyrus ussuriensis, P. bretscgneideri, P. pyraster, and P. elaegnifolia). Most of the accessions examined demonstrated the presence of unique allele sets. The degree of relationship between Russian and Western European pear cultivar was established. It was demonstrated that P. ussuriensis and its first generation progeny were genetically distant from typical cultivars of P. communis, as well as from the P. communis x P. ussuriensis hybrids of later generations. SSR estimates of the cultivar relatedness were shown to correlate with the corresponding pedigree-based estimates. A number of SSR alleles specific to P. ussuriensis were identified. Based on the analysis of microsatellite loci, the allelic composition was determined for each cultivar examined. These data can serve as a molecular certificate of the cultivar.

  7. A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird.

    PubMed

    Weinman, Lucia R; Solomon, Joseph W; Rubenstein, Dustin R

    2015-05-01

    The development of genetic markers has revolutionized molecular studies within and among populations. Although poly-allelic microsatellites are the most commonly used genetic marker for within-population studies of free-living animals, biallelic single nucleotide polymorphisms, or SNPs, have also emerged as a viable option for use in nonmodel systems. We describe a robust method of SNP discovery from the transcriptome of a nonmodel organism that resulted in more than 99% of the markers working successfully during genotyping. We then compare the use of 102 novel SNPs with 15 previously developed microsatellites for studies of parentage and kinship in cooperatively breeding superb starlings (Lamprotornis superbus) that live in highly kin-structured groups. For 95% of the offspring surveyed, SNPs and microsatellites identified the same genetic father, but only when behavioural information about the likely parents at a nest was included to aid in assignment. Moreover, when such behavioural information was available, the number of SNPs necessary for successful parentage assignment was reduced by half. However, in a few cases where candidate fathers were highly related, SNPs did a better job at assigning fathers than microsatellites. Despite high variation between individual pairwise relatedness values, microsatellites and SNPs performed equally well in kinship analyses. This study is the first to compare SNPs and microsatellites for analyses of parentage and relatedness in a species that lives in groups with a complex social and kin structure. It should also prove informative for those interested in developing SNP loci from transcriptome data when published genomes are unavailable.

  8. Polymorphic microsatellite loci isolated from Cervus unicolor (Cervidae) show inbreeding in a domesticated population of Taiwan Sambar deer.

    PubMed

    Lin, D Y; Chiang, T Y; Huang, C C; Lin, H D; Tzeng, S J; Kang, S R; Sung, H M; Wu, M C

    2014-05-23

    Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesticated Formosan Sambar deer (Cervus unicolor swinhoei). All loci were polymorphic, with 10-19 alleles per locus. The average observed heterozygosity across loci and samples was 0.310, ranging from 0 to 0.750 at each locus. All loci but one, CU18, deviated from Hardy-Weinberg equilibrium due to excessive homozygosity in these domesticated broodstocks, reflecting inbreeding. These microsatellite loci will be useful, not only for assessment of population structure and genetic variability, but also for conservation of wild deer populations in Taiwan.

  9. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  10. Association of apoptosis-related microsatellite polymorphisms on chromosome 1q in Taiwanese systemic lupus erythematosus patients

    PubMed Central

    Chen, J-Y; Wang, C-M; Lu, S-C; Chou, Y-H; Luo, S-F

    2006-01-01

    Apoptosis is important in the pathogenesis of systemic lupus erythematosus (SLE). Several genome-wide scan studies have suggested chromosome 1q as a genetic susceptibility locus for SLE. This study investigated the association of apoptosis-related genes on chromosome 1q, Fas ligand (FasL), interleukin (IL)-10 and poly(ADP-ribose) polymerase (PARP), promoter microsatellite multi-allelic polymorphisms with SLE susceptibility and clinical characteristics in Taiwan. This study recruited 237 SLE patients and 304 healthy controls. FasL, IL-10 and PARP promoter microsatellite polymorphisms were genotyped employing gene scan. IL-10, located on 1q31–32, emerged as a significant susceptibility gene locus in Taiwanese SLE (T4 statistic = 0·01). IL-10 CA21 allele was the most common allele of 15 identified in Taiwanese, displaying skewed distribution of susceptibility in Taiwanese SLE patients. Conversely, the IL-10 CA20 allele showed a protective effect of SLE susceptibility. Additionally, the IL-10 CA26 allele displayed a negative significant association with ascites and IL-10 CA25 allele increased the occurrence of the anti-cardiolipin IgM antibody. This study identified five alleles of FasL and nine alleles of PARP of microsatellite polymorphisms in Taiwanese patients. FasL and PARP alleles displayed no skewing distribution between Taiwanese SLE patients and controls. However, FasL GT15 and PARP CA17 allele demonstrated a high discoid rash presentation (T4 statistic 0·01 and 0·03, respectively) and PARP CA12 allele displayed a significant association with anti-cardiolipin IgM antibody production (T4 statistic 0·02). IL-10, FasL and PARP microsatellite polymorphisms exhibited significant associations with SLE susceptibility and/or clinical characteristics in Taiwanese patients. Thus, SLE is a complex and multiple genetics determined autoimmune disease. Chromosome 1q23–42 is an important genetic locus for further SLE subphenotype susceptibility study. PMID:16412052

  11. Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

    USGS Publications Warehouse

    Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

    2009-01-01

    Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

  12. Conservation of human chromosome 13 polymorphic microsatellite (CA){sub n} repeats in chimpanzees

    SciTech Connect

    Deka, R.; Shriver, M.D.; Yu, L.M.

    1994-07-01

    Tandemly repeated (dC-dA){sub n} {center_dot} (dG-dT){sub n} sequences occur abundantly and are found in most eukaryotic genomes. To investigate the level of conservation of these repeat sequences in nonhuman primates, the authors have analyzed seven human chromosome 13 dinucleotide (CA){sub n} repeat loci in chimpanzees by DNA amplification using primers designed for analysis of human loci. Comparable levels of polymorphism at these loci in the two species, revealed by the number of alleles, heterozygosity, and allele sizes, suggest that the (CA){sub n} repeat arrays and their genomic locations are highly conserved. Even though the proportion of shared alleles between the two species varies enormously and the modal alleles are not the same, allelic lengths at each locus in the chimpanzees are detected within the bounds of the allele size range observed in humans. A similar observation has been noted in a limited number of gorillas and orangutans. Using a new measure of genetic distance that takes into account the size of alleles, they have compared the genetic distance between humans and chimpanzees. The genetic distance between these two species was found to be ninefold smaller than expected assuming there is no selection or mutational bias toward retention of (CA){sub n} repeat arrays. These findings suggest a functional significance for these microsatellite loci. 34 refs., 1 fig., 2 tabs.

  13. Refining the position of Wilson disease by linkage disequilibrium with polymorphic microsatellites.

    PubMed Central

    Bowcock, A. M.; Tomfohrde, J.; Weissenbach, J.; Bonne-Tamir, B.; St George-Hyslop, P.; Giagheddu, M.; Cavalli-Sforza, L. L.; Farrer, L. A.

    1994-01-01

    Wilson disease (WND) is an autosomal recessive disorder that is due to an inability of the liver to eliminate copper. Copper buildup in the liver, brain, kidney, and other tissues can result in liver cirrhosis, neurologic and psychiatric defects, and other problems. We have localized the disease-containing region to between D13S31 and D13S59, with > 70 multiply affected families, and have constructed a YAC contig of > 4.5 Mb that spans these loci and orders nine highly polymorphic microsatellites. Here we present an analysis of disequilibrium with markers in this interval and provide evidence for strong allelic associations between AFM084xc5 alleles and WND alleles in European, Middle Eastern, and East Asian populations. Significant but weaker allelic associations were also observed between WND alleles and alleles at D13S137 and D13S169. The strength of the association between AFM084xc5 and WND in all non-Sardinian populations combined (linkage-disequilibrium coefficient [phi] = .61) suggests that the number of mutations accounting for WND is less than expected on the basis of the variety of clinical symptoms that are observed. PMID:8279473

  14. Refining the position of Wilson disease by linkage disequilibrium with polymorphic microsatellites

    SciTech Connect

    Bowcock, A.M.; Tomfohrde, J. ); Weissenbach, J. ); Bonne-Tamir, B.; George-Hyslop, P.; Giagheddu, M.; Cavalli-Sforza, L.L.; Farrer, L.A.

    1994-01-01

    Wilson disease (WND) is an autosomal recessive disorder that is due to an inability to the liver to eliminate copper. Copper buildup in the liver, brain, kidney, and other tissues can result in liver cirrhosis, neurologic and psychiatric defects, and other problems. The authors have localized the disease-containing region to between D13S31 and D13S59, with >70 multiply affected families, and have constructed a YAC contig of >4.5 Mb that spans these loci and orders nine highly polymorphic microsatellites. Here, the authors present an analysis of disequilibrium with markers in this interval and provide evidence for strong allelic associations between AFM084[times]c5 alleles and WND allels in European, Middle Eastern, and East Asian populations. Significant but weaker allelic associations were also observed between WND alleles and alleles at D13S137 and D13S169. The strength of the association between AFM084[times]c5 and WND in all non-Sardinian populations combined (linkage-disequilibrium coefficient [[theta

  15. Microsatellite polymorphism and its association with body weight and selected morphometrics of farm red fox (Vulpes vulpes L.).

    PubMed

    Zatoń-Dobrowolska, Magdalena; Mucha, Anna; Wierzbicki, Heliodor; Morrice, David; Moska, Magdalena; Dobrowolski, Maciej; Przysiecki, Piotr

    2014-11-01

    Polymorphism of 30 canine-derived microsatellites was studied in a group of 200 red foxes kept on 2 Polish farms. 22 out of 30 microsatellites were selected to study association between marker genotypes and body weight (BW), body length (BL), body circumference (BC), tail length (TL), ear height (EH), length of the right front limb (FRLL), length of the right rear limb (RRLL), length of the right front foot (FRFL) and length of the right rear foot (RRFL). A total of 112 alleles and 243 genotypes were found at 22 autosomal microsatellite loci. Three monomorphic loci deemed as uninformative were excluded from the study. The association between marker genotypes and the studied traits was analysed using general linear model (GLM) procedure and least squares means (LSM). Linkage disequilibrium (LD) was estimated to assess non-random association between microsatellite loci. Out of 19 microsatellites studied four markers showed no association with the studied traits, three markers had a significant effect on one trait, and another three markers had significant effect on two traits. Among ten microsatellites with significant effect on four economically important traits (BW, BL, BC, TL) four were associated with two characters: marker FH2613 with BW and BC, marker FH2097withBL and BC, marker ZUBECA6 with BW and BC, whereas marker REN75M10 was associated with BL and TL. The strongest LD (r(2) ranged from 0.15 to 0.33) was estimated between nine loci with significant effect on economically important traits (BW, BL, BC, TL).

  16. Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study.

    PubMed

    Mishra, Sudhanshu; Singh, Sujeet Kumar; Munjal, Ashok Kumar; Aspi, Jouni; Goyal, Surendra Prakash

    2014-01-03

    In India, six landscapes and source populations that are important for long-term conservation of Bengal tigers (Panthera tigris tigris) have been identified. Except for a few studies, nothing is known regarding the genetic structure and extent of gene flow among most of the tiger populations across India as the majority of them are small, fragmented and isolated. Thus, individual-based relationships are required to understand the species ecology and biology for planning effective conservation and genetics-based individual identification has been widely used. But this needs screening and describing characteristics of microsatellite loci from DNA from good-quality sources so that the required number of loci can be selected and the genotyping error rate minimized. In the studies so far conducted on the Bengal tiger, a very small number of loci (n = 35) have been tested with high-quality source of DNA, and information on locus-specific characteristics is lacking. The use of such characteristics has been strongly recommended in the literature to minimize the error rate and by the International Society for Forensic Genetics (ISFG) for forensic purposes. Therefore, we describe for the first time locus-specific genetic and genotyping profile characteristics, crucial for population genetic studies, using high-quality source of DNA of the Bengal tiger. We screened 39 heterologous microsatellite loci (Sumatran tiger, domestic cat, Asiatic lion and snow leopard) in captive individuals (n = 8), of which 21 loci are being reported for the first time in the Bengal tiger, providing an additional choice for selection. The mean relatedness coefficient (R = -0.143) indicates that the selected tigers were unrelated. Thirty-four loci were polymorphic, with the number of alleles ranging from 2 to 7 per locus, and the remaining five loci were monomorphic. Based on the PIC values (> 0.500), and other characteristics, we suggest that 16 loci (3 to 7 alleles) be used for genetic

  17. Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

    PubMed Central

    Ananda, Guruprasad; Hile, Suzanne E.; Breski, Amanda; Wang, Yanli; Kelkar, Yogeshwar; Makova, Kateryna D.; Eckert, Kristin A.

    2014-01-01

    Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation. However, human polymorphism levels at interrupted microsatellites (iMSs) are not known at a genome-wide scale, and the pathways for gaining interruptions are poorly understood. Using the 1000 Genomes Phase-1 variant call set, we interrogated mono-, di-, tri-, and tetranucleotide repeats up to 10 units in length. We detected ∼26,000–40,000 iMSs within each of four human population groups (African, European, East Asian, and American). We identified population-specific iMSs within exonic regions, and discovered that known disease-associated iMSs contain alleles present at differing frequencies among the populations. By analyzing longer microsatellites in primate genomes, we demonstrate that single interruptions result in a genome-wide average two- to six-fold reduction in microsatellite mutability, as compared with perfect microsatellites. Centrally located interruptions lowered mutability dramatically, by two to three orders of magnitude. Using a biochemical approach, we tested directly whether the mutability of a specific iMS is lower because of decreased DNA polymerase strand slippage errors. Modeling the adenomatous polyposis coli tumor suppressor gene sequence, we observed that a single base substitution interruption reduced strand slippage error rates five- to 50-fold, relative to a perfect repeat, during synthesis by DNA polymerases α, β, or η. Computationally, we demonstrate that iMSs arise primarily by base substitution mutations within individual human genomes. Our biochemical survey of human DNA polymerase α, β, δ, κ, and η error rates within certain microsatellites suggests that interruptions are created most frequently by low fidelity polymerases. Our combined computational and biochemical results demonstrate that iMSs are abundant in human genomes and are sources of population-specific genetic variation that may affect genome stability. The

  18. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

    PubMed Central

    Jan, Catherine

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

  19. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

    PubMed

    Jan, Catherine; Fumagalli, Luca

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  20. Rapid development of polymorphic microsatellite markers for the Amur sturgeon (Acipenser schrenckii) using next-generation sequencing technology.

    PubMed

    Li, L M; Wei, L; Jiang, H Y; Zhang, Y; Zhang, X J; Yuan, L H; Chen, J P

    2015-07-14

    Anthropogenic activities have seriously impacted wild resources of the Amur sturgeon, Acipenser schrenckii, and more information on local and regional population genetic structure is required to aid the conservation of this species. In this study, we report the development of 12 novel polymorphic microsatellite loci using next-generation sequencing technology, and the genotyping of 24 individuals collected from a sturgeon farm. The results show that the mean number of ob-served alleles per locus is 6.6 (ranging from 2 to 17). Observed and expected heterozygosity values ranged from 0 to 0.958 and from 0.508 to 0.940, respectively. Not a single locus showed significant departure from Hardy-Weinberg equilibrium and no linkage disequilibrium was observed among any pairwise loci. These highly informative microsatellite markers will be useful for genetic diversity and population structure analyses of A. schrenckii and other species of this genus.

  1. Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing

    PubMed Central

    Fortuna, Taiadjana M.; Snirc, Alodie; Badouin, Hélène; Gouzy, Jérome; Siguenza, Sophie; Esquerre, Diane; Le Prieur, Stéphanie; Shykoff, Jacqui A.; Giraud, Tatiana

    2016-01-01

    Background Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i.e., with two independently segregating mating-type loci), while most of the anther-smut Microbotryum fungi are bipolar (i.e., with a single mating-type locus). Saponaria officinalis is a widespread long-lived perennial plant species with multiple flowering stems, which makes its anther-smut pathogen a good model for studying phylogeography and within-host multiple infections. Principal Findings Here, based on a generated genome sequence of M. saponariae we developed 6 multiplexes with a total of 22 polymorphic microsatellite markers using an inexpensive and efficient method. We scored these markers in fungal individuals collected from 97 populations across Europe, and found that the number of their alleles ranged from 2 to 11, and their expected heterozygosity from 0.01 to 0.58. Cross-species amplification was examined using nine other Microbotryum species parasitizing hosts belonging to Silene, Dianthus and Knautia genera. All loci were successfully amplified in at least two other Microbotryum species. Significance These newly developed markers will provide insights into the population genetic structure and the occurrence of within-host multiple infections of M. saponariae. In addition, the draft genome of M. saponariae, as well as one of the described markers will be useful resources for studying the evolution of the breeding systems in the genus Microbotryum and the

  2. Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites.

    PubMed

    John, Sally; Shephard, Neil; Liu, Guoying; Zeggini, Eleftheria; Cao, Manqiu; Chen, Wenwei; Vasavda, Nisha; Mills, Tracy; Barton, Anne; Hinks, Anne; Eyre, Steve; Jones, Keith W; Ollier, William; Silman, Alan; Gibson, Neil; Worthington, Jane; Kennedy, Giulia C

    2004-07-01

    Despite the theoretical evidence of the utility of single-nucleotide polymorphisms (SNPs) for linkage analysis, no whole-genome scans of a complex disease have yet been published to directly compare SNPs with microsatellites. Here, we describe a whole-genome screen of 157 families with multiple cases of rheumatoid arthritis (RA), performed using 11,245 genomewide SNPs. The results were compared with those from a 10-cM microsatellite scan in the same cohort. The SNP analysis detected HLA*DRB1, the major RA susceptibility locus (P=.00004), with a linkage interval of 31 cM, compared with a 50-cM linkage interval detected by the microsatellite scan. In addition, four loci were detected at a nominal significance level (P<.05) in the SNP linkage analysis; these were not observed in the microsatellite scan. We demonstrate that variation in information content was the main factor contributing to observed differences in the two scans, with the SNPs providing significantly higher information content than the microsatellites. Reducing the number of SNPs in the marker set to 3,300 (1-cM spacing) caused several loci to drop below nominal significance levels, suggesting that decreases in information content can have significant effects on linkage results. In contrast, differences in maps employed in the analysis, the low detectable rate of genotyping error, and the presence of moderate linkage disequilibrium between markers did not significantly affect the results. We have demonstrated the utility of a dense SNP map for performing linkage analysis in a late-age-at-onset disease, where DNA from parents is not always available. The high SNP density allows loci to be defined more precisely and provides a partial scaffold for association studies, substantially reducing the resource requirement for gene-mapping studies.

  3. Microsatellite polymorphism in the P1 promoter region of the IGF-1 gene is associated with endometrial cancer

    PubMed Central

    KWASNIEWSKI, WOJCIECH; GOZDZICKA-JOZEFIAK, ANNA; WOLUN-CHOLEWA, MARIA; POLAK, GRZEGORZ; SIEROCINSKA-SAWA, JADWIGA; KWASNIEWSKA, ANNA; KOTARSKI, JAN

    2016-01-01

    Endometrial carcinoma (EC) is the most common type of gynecological malignancy. Studies have demonstrated that the insulin growth factor (IGF) pathway is implicated in the development of endometrial tumors and that the serum levels of IGF-1 are affected by estrogen. Most EC cells with high microsatellite instability (MSI-H) accumulate mutations at a microsatellite sequence in the IGF-1 gene. The present study investigated the CA repeat polymorphism in the P1 promoter region of the IGF-1 gene among Caucasian females with endometrial hyperplasia, EC and healthy control subjects, whose blood serum and surgical tissue specimens were analyzed. Differences or correlations between the analyzed parameters [serum levels of IGF-1 and IGF binding protein (IGFBP)-1 and IGFBP-3 as well as estrogens among the polymorphisms] were verified using the χ2, Mann-Whitney U, Kruskal-Wallis or Spearman's rank correlation tests. A PCR amplification and DNA sequencing analysis was used for identification of (CA)n repeats in the P1 region of IGF-1. ELISA was used to determine the blood serum levels of IGF-1, IGFBP-1, IGFBP-3 and estrogens. Furthermore, IGF-1 was assessed in endometrial tissues by immunohistochemical analysis. The present study indicated no statistically significant differences between serum levels of IGF-1, IGFBP-1, IGFBP-3 and estrone, estriol and estradiol in the control and study groups. A significant correlation was identified between the IGF-1 levels and estrone levels in the MSI-H polymorphism (r=−0.41, P=0.012) as well as a highly negative correlation between IGF-1 levels and the estradiol levels in the MSI-H polymorphism (r=−0.6, P=0.002). Genotypes without the 19 CA allele were predominantly found in EC. Furthermore, statistical analysis indicated that the number of IGF-1-expressing cells was significantly elevated in MSI-H type 18-20 (P= 0.0072), MSI-L type 19-20 (P=0.025) and microsatellite-stable MSS type 19-19 (P=0.024) compared with those in the MSI-H 20

  4. Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus).

    PubMed

    Bertolotti, Alicia C; Griffiths, Sarah M; Truelove, Nathan K; Box, Stephen J; Preziosi, Richard F; Salinas de Leon, Pelayo

    2015-01-01

    The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11-49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

  5. Development of 10 highly-polymorphic microsatellite markers in the vulnerable Galápagos land iguanas (genus Conolophus).

    PubMed

    Rosa, Sabrina F P; Monteyne, Daniel; Milinkovitch, Michel C

    2009-01-01

    The two species of Galápagos land iguanas (Conolophus subcristatus and C. pallidus) are listed as 'vulnerable' species by the International Union for the Conservation of Nature (IUCN Red List; http://www.iucnredlist.org). Here, we report on the isolation and characterization of 10 microsatellite markers using 562 individuals sampled on all Galápagos islands where Conolophus species occur today. We show that these 10 loci are highly polymorphic and display diagnostic alleles for five out of the six island populations. These markers will be useful for Conolophus population genetic analyses as well as for guiding ongoing captive breeding programmes.

  6. PERMANENT GENETIC RESOURCES: Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum.

    PubMed

    Giraud, T; Yockteng, R; Marthey, S; Chiapello, H; Jonot, O; Lopez-Villavicencio, M; DE Vienne, D M; Hood, M E; Refregier, G; Gendrault-Jacquemard, A; Wincker, P; Dossat, C

    2008-03-01

    We report the development of 60 microsatellite markers on four species of the fungal complex Microbotryum, causing anther smut of the Caryophyllaceae. Microsatellites were found in four expressed sequence tag (EST) libraries, built from isolates of M. lychnis-dioicae, M. violaceum sensus stricto, M. lagerheimii and M. dianthorum, collected, respectively, from the plants Silene latifolia, S. nutans, S. vulgaris and Dianthus carthusianorum. Intrapopulation polymorphism was investigated using 24 isolates, and cross-amplification was explored using 23 isolates belonging to at least 10 different Microbotryum species. This study provides numerous microsatellite markers for population genetics and mapping studies.

  7. Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing.

    PubMed

    Tadano, R; Nunome, M; Mizutani, M; Kawahara-Miki, R; Fujiwara, A; Takahashi, S; Kawashima, T; Nirasawa, K; Ono, T; Kono, T; Matsuda, Y

    2014-12-01

    Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.

  8. Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki).

    PubMed

    Tada, T; Seki, Y; Kameyama, Y; Kikkawa, Y; Wada, K

    2016-12-19

    The Ezo red fox (Vulpes vulpes schrencki), a subspecies endemic to Hokkaido island, Japan, is a known host species for the tapeworm Echinococcus multilocularis. To develop tools for molecular ecological studies, we isolated 28 microsatellite regions from the genome of Ezo red fox, and developed 18 polymorphic microsatellite markers. These markers were characterized using 7 individuals and 22 fecal samples of the Ezo red fox. The number of alleles for these markers ranged from 1 to 7, and the observed heterozygosity, estimated on the basis of the genotypes of 7 individuals, ranged from 0.29 to 1.00. All markers, except DvNok5, were in Hardy-Weinberg equilibrium (P > 0.05), and no linkage disequilibrium was detected among these loci, except between DvNok14 and DvNok28 (P = 0.01). Moreover, six microsatellite loci were successfully genotyped using feces-derived DNA from the Ezo red fox. The markers developed in our study might serve as a useful tool for molecular ecological studies of the Ezo red fox.

  9. Development and characterization of polymorphic microsatellite markers (SSRs) for an endemic plant, Pseudolarix amabilis (Nelson) Rehd. (Pinaceae).

    PubMed

    Geng, Qi-Fang; Liu, Jun; Sun, Lin; Liu, Hong; Ou-Yang, Yan; Cai, Ying; Tang, Xin-Sheng; Zhang, Hong-Wei; Wang, Zhong-Sheng; An, Shu-Qing

    2015-02-04

    Pseudolarix (Pinaceae) is a vulnerable (sensu IUCN) monotypic genus restricted to southeastern China. To better understand levels of genetic diversity, population structure and gene flow among populations of P. amabilis, we developed five compound SSR markers and ten novel polymorphic expressed sequence tags (EST) derived microsatellites. The results showed that all 15 loci were polymorphic with the number of alleles per locus ranging from two to seven. The expected and observed heterozygosities varied from 0.169 to 0.752, and 0.000 to 1.000, respectively. The inbreeding coefficient ranged from -0.833 to 1.000. These markers will contribute to research on genetic diversity and population genetic structure of P. amabilis, which in turn will contribute to the species conservation.

  10. First Insights into the Genetic Diversity of the Pinewood Nematode in Its Native Area Using New Polymorphic Microsatellite Loci

    PubMed Central

    Mallez, Sophie; Castagnone, Chantal; Espada, Margarida; Vieira, Paulo; Eisenback, Jonathan D.; Mota, Manuel; Guillemaud, Thomas; Castagnone-Sereno, Philippe

    2013-01-01

    The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed. PMID:23554990

  11. New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations.

    PubMed

    Kim, E M; An, H S; Kang, J H; An, C M; Dong, C M; Hong, Y K; Park, J Y

    2014-10-07

    Manila clam (Ruditapes philippinarum) is a valuable and intensively exploited shellfish species in Korea. Despite its importance, information on its genetic background is scarce. For the genetic characterization of R. philippinarum, expressed sequence tag-derived microsatellite markers were developed using next-generation sequencing. A total of 5879 tandem repeats containing di- to hexanucleotide repeat motifs were obtained from 236,746 reads (mean = 413 bp). Of the 62 loci screened, 24 (38.7%) were successfully amplified, and 10 were polymorphic in 144 individuals from 2 manila clam populations (Incheon and Geoje, Korea). The number of alleles ranged from 2 to 17 in the Incheon population and from 3 to 13 in the Geoje population (overall AR = 7.21). The mean observed and expected heterozygosities were estimated to be 0.402 and 0.555, respectively. Hence, there is less genetic variability in the Geoje population than in the Incheon population, although no significant reductions of genetic diversity were found between the populations (P > 0.05). However, significant genetic differentiation was detected between the populations (FST = 0.064, P < 0.001). Significant deviations from Hardy-Weinberg equilibrium and high inbreeding coefficients (mean FIS = 0.22-0.26) were detected in both populations. The 10 novel polymorphic microsatellite loci used in this study will be useful for future genetic mapping studies and for characterizing population structures, monitoring genetic diversity for successful aquaculture management, and developing conservation strategies for manila clam populations in Korea.

  12. Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites.

    PubMed

    Tsagkarakou, A; Tsigenopoulos, C S; Gorman, K; Lagnel, J; Bedford, I D

    2007-02-01

    The genetic polymorphism and the biotype identity of the tobacco whitefly Bemisia tabaci (Gennadius) have been studied in population samples taken from different localities within Greece from cultivated plants growing in greenhouses or in open environments and from non-cultivated plants. Two different approaches were used: sequencing of the mitochondrial cytochrome oxidase I (mtCOI) gene and genotyping using microsatellite markers. Analyses of the mtCOI sequences revealed a high homogeneity between the Greek samples which clustered together with Q biotype samples that had been collected from other countries. When genetic polymorphism was examined using six microsatellite markers, the Greek samples, which were all characterized as Q biotype were significantly differentiated from each other and clustered into at least two distinct genetic populations. Moreover, based on the fixed differences revealed by the mtCOI comparison of known B. tabaci biotype sequences, two diagnostic tests for discriminating between Q and B and non-Q/non-B biotypes were developed. Implementation of these diagnostic tools allowed an absence of the B biotype and presence of the Q biotype in the Greek samples to be determined.

  13. Isolation and characterisation of 11 polymorphic microsatellite markers in Papaver rhoeas L. (Corn Poppy), a major annual plant species from cultivated areas.

    PubMed

    Kati, Vaya; Corre, Valérie Le; Michel, Séverine; Jaffrelo, Lydia; Poncet, Charles; Délye, Christophe

    2012-12-24

    Papaver rhoeas, an annual plant species in the Papaveraceae family, is part of the biodiversity of agricultural ecosystems and also a noxious agronomic weed. We developed microsatellite markers to study the genetic diversity of P. rhoeas, using an enriched microsatellite library coupled with 454 next-generation sequencing. A total of 13,825 sequences were obtained that yielded 1795 microsatellite loci. After discarding loci with less than six repeats of the microsatellite motif, automated primer design was successful for 598 loci. We tested 74 of these loci for amplification with a total of 97 primer pairs. Thirty loci passed our tests and were subsequently tested for polymorphism using 384 P. rhoeas plants originating from 12 populations from France. Of the 30 loci, 11 showed reliable polymorphism not affected by the presence of null alleles. The number of alleles and the expected heterozygosity ranged from 3 to 7.4 and from 0.27 to 0.73, respectively. A low but significant genetic differentiation among populations was observed (F(ST) = 0.04; p < 0.001). The 11 validated polymorphic microsatellite markers developed in this work will be useful in studies of genetic diversity and population structure of P. rhoeas, assisting in designing management strategies for the control or the conservation of this species.

  14. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    PubMed

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences.

  15. Characterization of 22 highly polymorphic microsatellite loci in the cosmopolitan fungal plant pathogen Verticillium dahliae. Permanent Genetic Resources added to Molecular Ecology Resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twenty-two microsatellite loci were characterized in the soilborne plant pathogenic fungus Verticillium dahliae by analysis of the genome sequence. All loci were polymorphic in at least two of three populations of V. dahliae tested and collected from lettuce, spinach and tomato. These loci were us...

  16. CHARACTERIZATION OF SEVEN POLYMORPHIC MICROSATELLITE LOCI IN THE COMMON LOON (GAVIA IMMER)

    EPA Science Inventory

    We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from ten locations in North America, including breeding, migration stopover, and...

  17. Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker.

    PubMed

    Garcia-Hermoso, Dea; MacCallum, Donna M; Lott, Timothy J; Sampaio, Paula; Serna, Maria-José Buitrago; Grenouillet, Fréderic; Klaassen, Corné H W; Bretagne, Stéphane

    2010-07-01

    Microsatellite-based genotyping for Candida albicans can give discrepant results between laboratories when expressed in fragment sizes, because their determination depends on electrophoretic conditions. The interlaboratory reproducibility was assessed in six laboratories provided with an allelic ladder. Despite variations in size determinations, alleles were correctly assigned, making data transportable between laboratories.

  18. High resolution melting detects sequence polymorphism in rubus occidentalis L. monomorphic microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. However, primer pairs designed from the regions that flank SSRs often generate fragment...

  19. Multicenter Collaborative Study for Standardization of Candida albicans Genotyping Using a Polymorphic Microsatellite Marker▿

    PubMed Central

    Garcia-Hermoso, Dea; MacCallum, Donna M.; Lott, Timothy J.; Sampaio, Paula; Serna, Maria-José Buitrago; Grenouillet, Fréderic; Klaassen, Corné H. W.; Bretagne, Stéphane

    2010-01-01

    Microsatellite-based genotyping for Candida albicans can give discrepant results between laboratories when expressed in fragment sizes, because their determination depends on electrophoretic conditions. The interlaboratory reproducibility was assessed in six laboratories provided with an allelic ladder. Despite variations in size determinations, alleles were correctly assigned, making data transportable between laboratories. PMID:20427694

  20. DNA polymorphisms at bermudagrass microsatellite loci and their use in genotype fingerprinting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The economically important, turf-type bermudagrasses include diploid Cynodon transvaalensis, tetraploid C. dactylon, and sterile triploid hybrids produced by crosses of these species. The objective of this study was to develop a set of microsatellite markers that could be used to distinguish among c...

  1. De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, Silonia silondia (Hamilton, 1822) and their validation for population genetic studies.

    PubMed

    Mandal, Sangeeta; Jena, J K; Singh, Rajeev K; Mohindra, Vindhya; Lakra, W S; Deshmukhe, Geetanjali; Pathak, Abhinav; Lal, Kuldeep K

    2016-02-01

    The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity-capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6-24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall FST = 0.075; P < 0.0001) with maximum variation (92.5%) within populations. Cross-priming assessment revealed successful amplification (35-38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.

  2. Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.

    PubMed

    Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

    2015-02-13

    Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin.

  3. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    PubMed

    Khajuria, Yash Paul; Saxena, Maneesha S; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest

  4. Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae)

    PubMed Central

    de Castro e Souza, Andiara Silos Moraes; Miño, Carolina Isabel; Del Lama, Silvia Nassif

    2012-01-01

    We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (2–10 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and FST value showed weak genetic structuring (FST = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species. PMID:22481877

  5. Genetic differentiation among 6 populations of red deer (Cervus elaphus L.) in Poland based on microsatellite DNA polymorphism.

    PubMed

    Radko, Anna; Zalewski, D; Rubiś, Dominika; Szumiec, Agnieszka

    2014-12-01

    Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is DNA analysis, which allows for direct determination of the differences and changes within a group of animals. Because the analysis of microsatellite polymorphism in different Cervidae populations revealed considerable genetic variability in individual populations, it was important to test a set of markers in animals from these populations.The study was performed with muscle tissue and blood samples collected from a total of 793 red deer. Six groups (subpopulations) of red deer were defined according to region: Masurian (330 animals), Bieszczady (194 animals), Małopolska (80 animals), Sudety (76 animals), Lower Silesian (62 animals) and Lubusz (51 animals). The analysis involved 12 STR markers (BM1818, OarAE129, OarFCB5, OarFCB304, RM188, RT 1, RT 13, T26, T156, T193, T501, TGLA53), for which conditions for simultaneous amplification were established.Based on this study, it is concluded that the chosen set of 12 microsatellite markers could be used to evaluate the genetic structure and to monitor changes in Poland's red deer population.

  6. Analysis of microsatellite polymorphism around the HLA-B locus in Iranian patients with Behçet's disease.

    PubMed

    Mizuki, N; Yabuki, K; Ota, M; Katsuyama, Y; Ando, H; Nomura, E; Funakoshi, K; Davatchi, F; Chams, H; Nikbin, B; Ghaderi, A A; Ohno, S; Inoko, H

    2002-11-01

    We have previously suggested that in a Japanese population the susceptible locus for Behçet's disease (BD) is HLA-B51 itself. To confirm this finding in another population, we performed HLA class I typing using the PCR-SSP method and analyzed eight polymorphic markers distributed within 1100 kb around the HLA-B gene using automated sequencer and subsequent automated fragment detection by fluorescent-based technology with the DNA samples of 84 Iranian patients with BD and 87 healthy ethnically matched controls. As a result, three microsatellite alleles (MICA-A6, MIB-348, C1-4-1-217) and HLA-B51 were found to be strongly associated with BD. Of these alleles HLA-B51 is the most strongly associated allele. There were no alleles that were increased in allele frequency at any microsatellite loci centromeric of MICA or telomeric of HLA-B51. Therefore, HLA-B51 was confirmed to be by far the most strongly associated gene with BD in an Iranian population.

  7. Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000.

    PubMed

    Sacks, Benjamin N; Lounsberry, Zachary T; Kalani, Tatyana; Meredith, Erin P; Langner, Cristen

    2016-01-01

    The tule elk (Cervus elaphus nannodes) experienced a severe bottleneck in the 1800s, resulting in low genetic diversity. There is a need for high-resolution genetic assays that can be used to differentiate individual elk, including close relatives, with high confidence. An efficient assay requires multiple markers both polymorphic and that can be amplified in concert with other markers in multiplex reactions. To develop such markers, we employed 150-bp paired-end whole genome shotgun sequencing on an Illumina HiSeq3000 platform to discover dinucleotide microsatellite markers. After preliminary screening of these markers, we selected and screened 15 candidate loci and 5 existing tetra nucleotide markers in 56 tule elk. We combined these markers in 2 multiplex reactions and report primer concentrations and PCR conditions enabling their efficient amplification.

  8. Analysis of microsatellite polymorphisms within the GLC1F locus in Japanese patients with normal tension glaucoma

    PubMed Central

    Murakami, Kaori; Ota, Masao; Shiota, Tomoko; Nomura, Naoko; Kashiwagi, Kenji; Mabuchi, Fumihiko; Iijima, Hiroyuki; Kawase, Kazuhide; Yamamoto, Tetsuya; Nakamura, Makoto; Negi, Akira; Sagara, Takeshi; Nishida, Teruo; Inatani, Masaru; Tanihara, Hidenobu; Aihara, Makoto; Araie, Makoto; Fukuchi, Takeo; Abe, Haruki; Higashide, Tomomi; Sugiyama, Kazuhisa; Kanamoto, Takashi; Kiuchi, Yoshiaki; Iwase, Aiko; Ohno, Shigeaki; Inoko, Hidetoshi; Mizuki, Nobuhisa

    2010-01-01

    Purpose To investigate whether the GLC1F locus is associated with normal tension glaucoma (NTG) in Japanese patients. Methods We recruited 242 unrelated Japanese subjects, including, 141 NTG patients and 101 healthy controls. The patients exhibiting a comparatively early onset were selected as they suggest that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 11 highly polymorphic microsatellite markers in and around the GLC1F locus. Results Individuals carrying the 163 allele of D7S1277i had a statistically significant increased risk of NTG (p=0.0013, pc=0.016, OR=2.47, 95%CI=1.42–4.30). None of the other markers identified significant loci (pc>0.05) after Bonferroni’s correction. Conclusions These findings suggested that the genes in the GLC1F locus may be associated with the pathogenesis of NTG. PMID:20309402

  9. Novel polymorphic microsatellite loci for distinguishing rock bass (Ambloplites rupestris), Roanoke bass (Ambloplites cavifrons), and their hybrids.

    PubMed

    Eschenroeder, Jackman C; Roberts, James H

    2016-10-01

    The rock bass (Ambloplites rupestris) is a popular sport-fish native to the Mississippi and Great Lakes basins of North America. The species has been widely introduced outside its native range, including into Atlantic-slope streams of Virginia where it may hybridize with an imperiled, similar-looking congener, the Roanoke bass (Ambloplites cavifrons). In this study, we identified and evaluated novel molecular markers to facilitate identification of these species and study the extent of hybridization. Using molecular libraries developed from A. rupestris, we identified a suite of candidate nuclear microsatellite loci, synthesized primer sets, and tested these markers for amplification and polymorphism in populations of both species. We then calculated standard diversity statistics within and differentiation statistics between species, the latter providing an indication of marker power for distinguishing the species and their hybrids. Additionally, we evaluated our efficiency for identifying hybrids by classifying simulated genotypes of known ancestry. Eleven loci were polymorphic (2-22 alleles per locus) and reliably amplified in both species. Multilocus genetic differentiation between A. cavifrons and A. rupestris was quite high (F ST  = 0.66; D LR  = 19.3), indicating the high statistical power of this marker set for species and hybrid identification. Analyses of simulated data suggested these markers reliably distinguish between hybrids and non-hybrids, as well as between F1 hybrids and backcrossed individuals. This panel of 11 loci should prove useful for understanding patterns of hybridization between A. rupestris and A. cavifrons. As the first microsatellite markers developed for Ambloplites, these markers also should prove broadly useful for population genetic studies of this genus.

  10. Polymorphic microsatellite markers in the outbred CFW and ICR stocks for the generation of speed congenic mice on C57BL/6 background.

    PubMed

    Teppner, I; Aigner, B; Schreiner, E; Müller, M; Windisch, M

    2004-10-01

    Reliable definition of the phenotype of particular alleles is carried out in the genetic background of inbred strains. Appearance of mutations in outbred mice therefore requires the generation of congenic mice. The aim of this study was the establishment of a list of polymorphic microsatellite markers which can be used in a polymerase chain reaction (PCR)-based marker-assisted selection protocol (MASP) to allow the use of the two common outbred stocks, CFW and ICR, as donor animals for the fast generation of congenic C57BL/6 mice. The selection of informative microsatellite markers was carried out to provide a simple evaluation of the PCR products by conventional agarose gel electrophoresis. Outbred mice from three suppliers were examined. In total, 153 microsatellite loci were analysed. Here we present 76 and 70 microsatellite markers polymorphic for the outbred ICR and CFW stocks compared to C57BL/6. At least three microsatellite loci per chromosome were chosen as informative markers for the autosomal genome, giving rise to a maximum marker distance of 58 cM. Thus, additional individual markers have to be selected for the respective outbred mouse which is chosen as a donor animal.

  11. Development of 14 microsatellite markers in Odontites vernus s.l. (Orobanchaceae) and cross-amplification in related taxa1

    PubMed Central

    Pinto-Carrasco, Daniel; Košnar, Jiří; López-González, Noemí; Koutecký, Petr; Těšitel, Jakub; Rico, Enrique; Martínez-Ortega, M. Montserrat

    2016-01-01

    Premise of the study: Microsatellite primers were developed for the first time in the root hemiparasite herb Odontites vernus (Orobanchaceae). These markers will be useful to investigate the role of polyploidization in the evolution of this diploid-tetraploid complex, as well as the extent of gene flow between different ploidy levels. Methods and Results: Fourteen polymorphic and reproducible loci were identified and optimized from O. vernus using a microsatellite-enriched library and 454 Junior sequencing. The set of primers amplified di- to pentanucleotide repeats and showed two to 13 alleles per locus. Transferability was tested in 30 taxa (19 belonging to Odontites and 11 from eight other genera of Orobanchaceae tribe Rhinantheae). Conclusions: The results indicate the utility of the newly developed microsatellites in O. vernus and several other species, which will be useful for taxon delimitation and conservation genetics studies. PMID:27011897

  12. Patterns of microsatellite polymorphism in the range-restricted bonobo (Pan paniscus): considerations for interspecific comparison with chimpanzees (P. troglodytes).

    PubMed

    Reinartz, G E; Karron, J D; Phillips, R B; Weber, J L

    2000-03-01

    The endangered great ape, Pan paniscus (bonobo) has the smallest range of the African apes. Virtually nothing is known about the genetic diversity or genetic structure of this species, while substantial amounts of polymorphism have been reported for the bonobo's widespread congener, the chimpanzee (P. troglodytes). Given its restricted range, what is the extent of genetic variation in the bonobo relative to the chimpanzee, and is the bonobo genetically depauperate? To investigate patterns of genetic polymorphism, bonobos of wild origin were genotyped for 28 microsatellite loci. The mean number of alleles per locus (5.2) and the mean observed heterozygosity (0.52) in bonobos were similar to variation observed in a wild chimpanzee community (P. t. schweinfurthii). The rarer bonobo is not genetically depauperate and may have genetic diversity comparable to the eastern chimpanzee subspecies. Bonobos have approximately 55% of the allelic diversity and 66% of the observed heterozygosity exhibited by all three chimpanzee subspecies sampled across equatorial Africa. Resampling techniques were used to quantify the effects of sample size differences and number and choice of loci between bonobos and chimpanzees. The examination of these variables underscores their importance in accurately interpreting interspecific comparisons of diversity estimates.

  13. Development and characterization of polymorphic microsatellite markers for Castanopsis hystrix (Fagaceae).

    PubMed

    Jiang, Y; Li, Z H; Zhu, J Y; Liu, H L

    2015-03-30

    Castanopsis hystrix is one of the most important and dominant species in evergreen broad-leaved forests in subtropical China. However, the population of this species undergone severe decline because of deforestation over the past 2 decades. For both conservation and forestry management, it is essential to develop molecular markers for C. hystrix. We identified 11 microsatellite loci in 2 wild populations. The number of alleles ranged from 3-11, with an average of 6.45 alleles per locus. The observed and expected heterozygosities ranged from 0.640-0.960 and from 0.676-0.910, respectively.

  14. A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.

    PubMed

    Mahfooz, Sahil; Srivastava, Arpita; Srivastava, Alok K; Arora, Dilip K

    2015-09-01

    We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents <1%. Among all classes of repeats, 36.5% motifs were found conserved within Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium.

  15. Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA

    PubMed Central

    SENJU, Natsuko; TOZAKI, Teruaki; KAKOI, Hironaga; SHINJO, Akihisa; MATSUYAMA, Ryota; ALMUNIA, Julio; TAKASU, Masaki

    2016-01-01

    Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0.999998. The second is the clarification of the current genetic diversity of Yonaguni horses. The average number of alleles, observed heterozygosity, expected heterozygosity and fixation index were 4.4, 0.591, 0.601 and 0.016, respectively, for the analyzed horses. The probability of a genetic bottleneck, under the assumptions of the stepwise mutation model, was 0.432, suggesting that the genetic structure of the horses was not influenced by a recent bottleneck. Genetic distance between individuals was visualized by a phylogenetic tree based on the proportion of shared alleles. Structure analysis based on Bayesian clustering revealed the possibility that Yonaguni horses comprise four or five subpopulations. Consequently, although only two haplotypes were identified in the mitochondrial analysis, genetic diversity of Yonaguni horses was not particularly low in comparison with that of other breeds that are at risk of extinction. PMID:28049866

  16. Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA

    PubMed Central

    SENJU, Natsuko; TOZAKI, Teruaki; KAKOI, Hironaga; ALMUNIA, Julio; MAEDA, Masami; MATSUYAMA, Ryota; TAKASU, Masaki

    2016-01-01

    To help plan conservation of the endangered Miyako horse, a biological resource of the Miyako Islands in Japan, we characterized the genetics of the breed by genotyping 32 microsatellites and identifying mitochondrial DNA haplotypes. We also calculated genetic distances between individuals based on the proportion of shared alleles and visualized the genetic relationships with a phylogenetic tree. Two important results were obtained. One is that accurate pedigree registration of the horse by using microsatellites is possible, as the exclusion power of parentage testing is 0.999998. Another is that the current genetic diversity of the horses was clarified. The average number of alleles, observed heterozygosity and expected heterozygosity were 4.2, 0.701 and 0.649, respectively, for the 35 analyzed horses. The probability values for bottleneck models (infinite allele model: 0.00000; stepwise mutation model: 0.00026; and two-phase model: 0.00000) suggested that Miyako horses have experienced a recent genetic bottleneck. Only one mitochondrial haplotype was identified. Consequently, genetic diversity within the population is relatively well-maintained despite a very small population size (41 at the time of the study), and the first priority in conservation of the Miyako horse is to increase the population size. PMID:27795462

  17. Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

    PubMed

    Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

    2016-09-02

    The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

  18. Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

    USGS Publications Warehouse

    Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, Brian L.; Reed, K.D.

    2011-01-01

    Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

  19. Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

    USGS Publications Warehouse

    Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

    2011-01-01

    Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

  20. Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci.

    PubMed

    Ciofi, Claudio; Tzika, Athanasia C; Natali, Chiara; Watts, Phillip C; Sulandari, Sri; Zein, Moch S A; Milinkovitch, Michel C

    2011-05-01

    Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.

  1. Geographic distribution of chromosome and microsatellite DNA polymorphisms in Oncorhynchus mykiss native to western Washington

    USGS Publications Warehouse

    Ostberg, C.O.; Thorgaard, G.H.

    1999-01-01

    Chromosome studies of native populations of Oncorhynchus mykiss (steelhead and rainbow trout) in western Washington and southern British Columbia revealed the presence of two evolutionarily distinct chromosome lineages. Populations between, and including, the Elwha River, Washington, and Chilliwack River, British Columbia, contained 2n = 60 chromosomes. Populations on the central Washington coast contained 2n = 58 chromosomes. The north Washington coast and western Strait of Juan de Fuca contained individuals with 58, 59, or 60 chromosomes, suggesting this is a transition zone between 58 and 60 chromosome groups. The differences in chromosomal structure between 2n = 58 and 2n = 60 groups are presumably a Robertsonian rearrangement and an inversion. Allelic variation at three microsatellite loci (One ??6, One ??11 and Omy 77) also was examined, and no significant variation was detected among the 58 and 60 chromosome races. A hypothesis is presented concerning the origin of the 60 chromosome lineage.

  2. Identification and validation of polymorphic microsatellite loci for the analysis of Phytophthora nicotianae populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A large number of SSR loci were screened in the genomic assemblies of 14 different isolates of Phytophthora nicotianae and primers were developed for amplification of 17 markers distributed among different contigs. These loci were highly polymorphic and amplified from genetically distant isolates of...

  3. [Intra- and interspecific polymorphism of (AAT)n in microsatellite locus du47D in parthenogenetic species of the genus Darevskia].

    PubMed

    Korchagin, V I; Vergun, A A; Godakova, S A; Tokarskaia, O N

    2013-03-01

    The molecular structure of the allelic variants of (AAT)n of the Du47D microsatellite locus was determined in parthenogenetic lizards Darevskia dahli, D. armeniaca, and D. rostombekovi. Comparative analysis of these alleles showed that they were characterized by perfect structure of microsatellite cluster, and were different in the number of (AAT) monomeric units, as well as in the combinations of species-specific substitutions and deletions in the microsatellite flanking regions. Molecular structure of microsatellite cluster, species-specific single nucleotide polymorphism (SNP), and different representation of alleles Du47 in the samples of parthenogenetic species examined point to the origin of the alleles from different bisexual species, which is consistent with the hybrid nature of unisexual species of the genus Darevskia. In addition, these data reflect different combination patterns of interspecific hybridization events with the participation of the same bisexual species upon the formation of hybrid genomes of parthenogenetic species. Possible application of the allelic variants of microsatellite loci of parthenogenetic lizards as the genetic markers for the analysis of the genomes of parthenogenetic species in the light of evolution, ecology, and parthenogenetic type of reproduction in vertebrates is discussed.

  4. Development of 12 novel polymorphic microsatellite markers using a next generation sequencing approach for Spiculopteragia spiculoptera, a nematode parasite of deer.

    PubMed

    Patrelle, Cécile; Jouet, Damien; Lehrter, Véronique; Ferté, Hubert

    2014-09-01

    Twelve novel polymorphic microsatellite markers were produced and characterized for Spiculopteragia spiculoptera (Nematoda, Trichostrongyloidae) a common parasite of abomasum of Roe and Red deer, using next generation sequencing approach, and two multiplexes PCR were developed with these markers. Polymorphism of each locus was tested in 40 individuals of this species from diverse wild populations of cervids, and was tested for crossed-amplification on four other species of nematodes, close to S. spiculoptera among the Trichostrongyloidea: 20 Spiculopteragia houdemeri, 34 Ostertagia leptospicularis, 16 Ashworthius sidemi, and 25 Trichostrongylus spp. Our new microsatellite markers seem to be specific to Spiculopteragia spiculoptera since no amplifications were obtained for the four other species. The number of alleles per locus ranged from 2 to 12, the average observed and expected heterozygosity per locus ranged from 0.025 to 0.641 and from 0.049 to 0.664, respectively. Four of the 12 microsatellite loci showed significant deviations from Hardy-Weinberg equilibrium (which two slightly significant). One locus pair showed significant linkage disequilibrium (Sspi4 vs. Sspi8). Neither evidence of scoring error due to stuttering nor evidence of large allele dropout was found at all of the 12 loci, but evidence of null alleles was indicated at three loci because of general excess of homozygotes for most allele size classes. These polymorphic loci will be useful markers to study population genetics structure of Spiculopteragia spiculoptera in order to understand transfer and to explain the relationships between deer populations.

  5. Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica.

    PubMed

    Wu, R X; Zhang, H R; Niu, S F; Zhai, Y; Liu, X F

    2016-11-21

    Sillago sihama (Forsskål, 1775), a commercially important marine fishery species in the Indo-West Pacific, is being developed as a target species for aquaculture and stock enhancement in China. However, due to the limitations of traditional isolation methods, the available microsatellite loci, or simple sequence repeats (SSRs), of S. sihama lack diversity. We used a stepwise approach including Illumina sequencing, primer screening, and SSR marker validation to develop diverse SSRs for S. sihama. A total of 853.48 Mb clean sequences were assembled with high coverage and sequencing depth, and 27,288 potential SSRs were identified. A set of 18 novel SSR markers with four type motifs including 11 di-, 1 tri-, 5 tetra-, and 1 hexanucleotide repeats were successfully isolated. The ranges of number of alleles per locus and observed and expected heterozygosities were 5-24, 0.226-0.968, and 0.319-0.950, respectively. The diversity parameters exhibited high levels of polymorphism in these 18 loci. Three loci with the presence of both null alleles and inbreeding showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni correction. Moreover, 13 loci developed in S. sihama showed high transferability to the closely related species Sillago japonica. The polymorphic SSR markers developed in this study may serve as valuable tools for further basic and applied research on the genetic resources of S. sihama as well as S. japonica. Our results indicate that this approach, based on next-generation sequencing technology, is convenient, cost-effective, and suitable for SSR marker isolation in other sillaginid fishes.

  6. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis

    PubMed Central

    Shell, Wyatt A.; Rehan, Sandra M.

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata’s distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator. PMID:27324584

  7. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis.

    PubMed

    Shell, Wyatt A; Rehan, Sandra M

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata's distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator.

  8. Fragmentation of sea bass populations in the western and eastern Mediterranean as revealed by microsatellite polymorphism.

    PubMed Central

    Bahri-Sfar, L; Lemaire, C; Ben Hassine, O K; Bonhomme, F

    2000-01-01

    We studied the genetic structure at six microsatellite loci of the Mediterranean sea bass (Dicentrarchus labrax) on 19 samples collected from different localities in the western and eastern Mediterranean basins. Significant divergence was found between the two basins. The distance tree showed two separate clusters of populations which matched well with geography, with the noticeable exception of one Egyptian sample which grouped within the western clade, a fact attributable to the introduction of aquaculture broodstock. No heterogeneity was observed within the western basin (theta = 0.0014 and n.s.). However, a significant level of differentiation was found among samples of the eastern Mediterranean (theta = 0.026 and p < 0.001). These results match with water currents but probably not with the dispersal abilities of this fish species. We thus hypothesize that selective forces are at play which limit long-range dispersal, a fact to be taken into account in the debate about speciation processes in the marine environment. PMID:10853737

  9. Isolation of polymorphic microsatellite loci for the marine invader Microcosmus squamiger (Ascidiacea).

    PubMed

    Rius, Marc; Turon, Xavier; Pascual, Marta

    2008-11-01

    The ascidian Microcosmus squamiger is native to Australia and has recently spread worldwide. It has become a pest in some littoral communities within its introduced range. An enriched genomic library of M. squamiger resulted in a total of eight polymorphic loci that were genotyped in 20 individuals from a population within its introduced range, and 20 individuals more from a native population. The mean number of alleles per locus was 5.33 and mean observed heterozygosity was 0.432. No significant linkage disequilibrium was found among loci pairs. Significant genetic differentiation was observed between populations.

  10. Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites

    PubMed Central

    Powell, W.; Morgante, M.; Doyle, J. J.; McNicol, J. W.; Tingey, S. V.; Rafalski, A. J.

    1996-01-01

    A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 +/- 0.088 and 0.159 +/- 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants. PMID:8889540

  11. Polymorphic microsatellite markers for the rare and endangered cactus Uebelmannia pectinifera (Cactaceae) and its congeneric species.

    PubMed

    Moraes, E M; Cidade, F W; Silva, G A R; Machado, M C

    2014-12-04

    The cactus genus Uebelmannia includes 3 narrow endemic species associated with rocky savanna habitats in eastern South America. Because of their rarity and illegal over-collection, all of these species are endangered. Taxonomic uncertainties resulting from dramatic local variation in morphology within Uebelmannia species preclude effective conservation efforts, such as the reintroduction or translocation of plants, to restore declining populations. In this study, we developed and characterized 18 perfect, dinucleotide simple-sequence repeat markers for U. pectinifera, the most widely distributed species in the genus, and tested the cross-amplification of these markers in the remaining congeneric species and subspecies. All markers were polymorphic in a sample from 2 U. pectinifera populations. The effective number of alleles ranged from 1.6 to 8.7, with an average per population of 3.3 (SE ± 0.30) and 4.5 (SE ± 0.50). Expected heterozygosity ranged from 0.375 to 0.847 and 8-10 loci showed departures from Hardy- Weinberg equilibrium in the analyzed populations. Based on the observed polymorphism level of each marker, as well as the analysis of null allele presence and evidence of amplification of duplicate loci, a subset of 12 loci can be used as reliable markers to investigate the genetic structure, diversity, and species limits of the Uebelmannia genus.

  12. Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans.

    PubMed

    Dhieb, C; Normand, A C; L'Ollivier, C; Gautier, M; Vranckx, K; El Euch, D; Chaker, E; Hendrickx, M; Dalle, F; Sadfi, N; Piarroux, R; Ranque, S

    2015-02-01

    Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI-TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI-TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well-characterized collection strains, using a Microflex(TM) system and Biotyper(TM) software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI-TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra-clade spectra recognition were unsuccessful. In conclusion, MALDI-TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI-TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory.

  13. Heme oxygenase-1 gene promoter microsatellite polymorphism is associated with progressive atherosclerosis and incident cardiovascular disease

    PubMed Central

    Pechlaner, Raimund; Willeit, Peter; Summerer, Monika; Santer, Peter; Egger, Georg; Kronenberg, Florian; Demetz, Egon; Weiss, Günter; Tsimikas, Sotirios; Witztum, Joseph L.; Willeit, Karin; Iglseder, Bernhard; Paulweber, Bernhard; Kedenko, Lyudmyla; Haun, Margot; Meisinger, Christa; Gieger, Christian; Müller-Nurasyid, Martina; Peters, Annette; Willeit, Johann; Kiechl, Stefan

    2015-01-01

    Objective The enzyme heme oxygenase-1 (HO-1) exerts cytoprotective effects in response to various cellular stressors. A variable number tandem repeat (VNTR) polymorphism in the HO-1 gene promoter region has previously been linked to cardiovascular disease (CVD). We examined this association prospectively in the general population. Approach and Results Incidence of stroke, myocardial infarction, or vascular death was registered between 1995 and 2010 in 812 participants of the Bruneck Study aged 45 to 84 years (49.4% males). Carotid atherosclerosis progression was quantified by high-resolution ultrasound. HO-1 VNTR length was determined by polymerase chain reaction. Subjects with ≥32 tandem repeats on both HO-1 alleles compared to the rest of the population (recessive trait) featured substantially increased CVD risk (hazard ratio [95% confidence interval], 5.45 (2.39, 12.42); P<0.0001), enhanced atherosclerosis progression (median difference in atherosclerosis score [interquartile range], 2.1 [0.8, 5.6] vs. 0.0 [0.0, 2.2] mm; P=0.0012), and a trend towards higher levels of oxidised phospholipids on apoB-100 (median OxPL/apoB level [interquartile range], 11364 [4160, 18330] vs. 4844 [3174, 12284] relative light units; P=0.0554). Increased CVD risk in those homozygous for ≥32 repeats was also detected in a pooled analysis of 7848 participants of the Bruneck, SAPHIR, and KORA prospective studies (HR [95% CI], 3.26 [1.50, 7.33]; P=0.0043). Conclusions This study found a strong association between the HO-1 VNTR polymorphism and CVD risk confined to subjects with a high number of repeats on both HO-1 alleles, and provides evidence for accelerated atherogenesis and decreased anti-oxidant defence in this vascular high-risk group. PMID:25359861

  14. Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12

    PubMed Central

    2009-01-01

    In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at 2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide (GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite markers. PMID:21637444

  15. Isolation and characterization of 20 polymorphic microsatellite loci in the migratory freshwater fish Leporinus obtusidens (Characiformes: Anostomidae) using 454 shotgun pyrosequencing.

    PubMed

    Villanova, G V; Vera, M; Díaz, J; Martinez, P; Calcaterra, N B; Arranz, S E

    2015-03-01

    Twenty polymorphic microsatellite markers were developed for the Neotropical fish Leporinus obtusidens using a next generation sequencing approach and tested in two other characifomes species, Schizodon platae and Prochilodus lineatus. Microsatellite loci alleles in L. obtusidens ranged between 2 and 20 alleles per locus (mean = 5·7), with expected heterozygosity values ranging from 0·097 to 0·956 (mean = 0·578) and observed heterozygosity values ranging from 0·000 to 0·800 (mean = 0·400) in a sample of 20 specimens from the lower Paraná River (Argentina). Most of these markers will be a valuable tool for captive breeding and stocking programmes, as well as for analyses of population connectivity and genetic structure in this broadly distributed Neotropical migratory fish.

  16. Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12.

    PubMed

    Murga-Zamalloa, Carlos; Guevara-Fujita, Maria Luisa; Estrada-Cuzcano, Alejandro; Fujita, Ricardo

    2009-10-01

    In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at 2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide (GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite markers.

  17. Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-Based typing of Candida albicans.

    PubMed

    Garcia-Hermoso, Dea; Cabaret, Odile; Lecellier, Gael; Desnos-Ollivier, Marie; Hoinard, Damien; Raoux, Dorothée; Costa, Jean-Marc; Dromer, Françoise; Bretagne, Stéphane

    2007-12-01

    For genotyping Candida albicans isolates, two PCR-based methods have recently emerged: multilocus sequence typing (MLST), based on the sequence of selected genes, and microsatellite length polymorphism (MLP), based on the length of PCR products containing variable numbers of short DNA repeats. To compare the two methods in their abilities to differentiate and group C. albicans isolates, we selected 50 independent isolates collected at the National Reference Center for Mycoses and Antifungals. MLST typing was performed using sequencing of seven loci as described at (http://test1.mlst.net). The MLP method consisted of a single multiplex PCR testing three different loci. Dendrograms were constructed by the unweighted pair group cluster method with Euclidean metric for both methods. The correlation between the distance matrices was performed with a Mantel test tested with 1,000 random permutations. The sensitivity and specificity of the MLP typing system were determined after allocating MLST groups for the greater number of isolates of each distinct MLP group. The discriminatory power index was >0.99, and the distances between the isolates were highly correlated with both systems. The Mantel coefficient and the Pearson product-moment correlation coefficient were 35,699 and 0.32, respectively (P < or = 1.2 x 10(-6)). Using MLP, the average specificity and sensitivity of clustering compared to MLST were 83% and 73%, respectively, when the singletons were excluded. The two methods are similarly discriminatory and can be interchangeable depending on the objectives. MLP is less expensive and faster than MLST. However, MLST is currently more accurate and additional standardization is needed for MLP.

  18. Characterisation of a novel panel of polymorphic microsatellite loci for the liver fluke, Fasciola hepatica, using a next generation sequencing approach.

    PubMed

    Cwiklinski, Krystyna; Allen, Katherine; LaCourse, James; Williams, Diana J; Paterson, Steve; Hodgkinson, Jane E

    2015-06-01

    The liver fluke, Fasciola hepatica is an economically important pathogen of sheep and cattle and has been described by the WHO as a re-emerging zoonosis. Control is heavily reliant on the use of drugs, particularly triclabendazole and as a result resistance has now emerged. The population structure of F. hepatica is not well known, yet it can impact on host-parasite interactions and parasite control with drugs, particularly regarding the spread of triclabendazole resistance. We have identified 2448 potential microsatellites from 83 Mb of F. hepatica genome sequence using msatfinder. Thirty-five loci were developed and optimised for microsatellite PCR, resulting in a panel of 15 polymorphic loci, with a range of three to 15 alleles. This panel was validated on genomic DNA from 46 adult F. hepatica; 38 liver flukes sourced from a Northwest abattoir, UK and 8 liver flukes from an established isolate (Shrewsbury; Ridgeway Research). Evidence for null alleles was found at four loci (Fh_1, Fh_8, Fh_13 and Fh_14), which showed markedly higher levels of homozygosity than the remaining 11 loci. Of the 38 liver flukes isolated from cattle livers (n=10) at the abattoir, 37 genotypes were identified. Using a multiplex approach all 15 loci could be amplified from several life cycle stages that typically yield low amounts of DNA, including metacercariae, the infective life cycle stage present on pasture, highlighting the utility of this multiplex microsatellite panel. This study reports the largest panel of microsatellite markers available to date for population studies of F. hepatica and the first multiplex panel of microsatellite markers that can be used for several life cycle stages.

  19. Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands

    PubMed Central

    Hosseinzadeh-Colagar, Abasalt; Haghighatnia, Mohammad Javad; Amiri, Zahra; Mohadjerani, Maryam; Tafrihi, Majid

    2016-01-01

    Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced ‘stutter products’ differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus) by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as ‘stutter bands’. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered. PMID:28097170

  20. Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands.

    PubMed

    Hosseinzadeh-Colagar, Abasalt; Haghighatnia, Mohammad Javad; Amiri, Zahra; Mohadjerani, Maryam; Tafrihi, Majid

    2016-09-01

    Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced 'stutter products' differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus) by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as 'stutter bands'. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered.

  1. Microsatellite and single nucleotide polymorphisms in the β-globin locus control region-hypersensitive Site 2: SPECIFICITY of Tunisian βs chromosomes.

    PubMed

    Ben Mustapha, Maha; Moumni, Imen; Zorai, Amine; Douzi, Kaïs; Ghanem, Abderraouf; Abbes, Salem

    2012-01-01

    The diversity of sickle cell disease severity is attributed to several cis acting factors, among them the single nucleotide polymorphisms (SNPs) and (AT) rich region in the β-locus control region (β-LCR). This contains five DNase I hypersensitive sites (HS) located 6 to 22 kb upstream to the ϵ gene. The most important of these is the HS2 (5' β-LCR-HS2), characterized by the presence of three different SNPs and a microsatellite region known to be in association with β(S) chromosomes in various populations. The aim of this study was to present the molecular investigation of the 5' β-LCR-HS2 site in normal and sickle cell disease individuals in order to determine if there is any correlation or specificity between these molecular markers, the β(S) Tunisian chromosomes and phenotypical expression of sickle cell disease. One hundred and twenty-four chromosomes from Tunisian individuals (49 β(S) carriers and 13 normal individuals) were screened by polymerase chain reaction (PCR) and sequencing for the polymorphic short tandem microsatellite repeats (AT)(X)N(12)(AT)(Y) and the three SNPs (rs7119428, rs9736333 and rs60240093) of the 5' β-LCR-HS2. Twelve configurations of the microsatellite motif were found with an ancestral configuration elaborated by ClustalW software. Normal and mutated alleles were observed at the homozygous and heterozygous states for the three SNPs. Correlation between microsatellites and SNPs suggests that mutant SNP alleles were mainly associated, in the homozygous sickle cell disease phenotype, with the (AT)(8)N(12)GT(AT)(7) configuration, whereas, normal SNP alleles were associated with the (AT)(X)N(12)(AT)(11) configurations in normal β(A) chromosomes. The correlation of these various configurations with Hb F expression was also investigated. The principal component analysis (PCA) showed the correlation between the homozygous sickle cell disease phenotype, mutated SNP alleles and the Benin microsatellite configuration (AT)(8)N(12)GT

  2. Microsatellite polymorphism in the heme oxygenase-1 promoter is associated with nonsevere and late-onset preeclampsia.

    PubMed

    Kaartokallio, Tea; Klemetti, Miira M; Timonen, Anni; Uotila, Jukka; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Lakkisto, Päivi; Laivuori, Hannele

    2014-07-01

    Preeclampsia is a serious and phenotypically heterogeneous vascular pregnancy disorder. Heme oxygenase-1 (HO-1) is a stress response enzyme that may protect the maternal endothelium and facilitate adequate metabolic adaptation to pregnancy by its antioxidant and anti-inflammatory functions. HO-1 stress response is modulated by HO-1 gene (HMOX1) polymorphisms. Individuals with the long allele of a guanine-thymine (GTn) microsatellite repeat located in the promoter region of HMOX1 have a higher risk of cardiometabolic diseases compared with those with the short allele. We investigated whether the long GTn allele of HMOX1 is associated with subtypes of preeclampsia. The GTn repeat was genotyped in 759 patients and in 779 controls from the Finnish Genetics of Preeclampsia Consortium (FINNPEC) cohort using DNA fragment analysis. In subtype analyses, the long-long (LL) genotype was associated with nonsevere (additive model: odds ratio [OR], 1.94; 95% confidence interval [CI], 1.13-3.31; recessive model: OR, 1.39; 95% CI, 1.02-1.89) and late-onset (additive model: OR, 1.44; 95% CI, 1.02-2.05; recessive model: OR, 1.28; 95% CI, 1.02-1.59) preeclampsia and with preeclampsia without a small-for-gestational-age infant (recessive model: OR, 1.27; 95% CI, 1.02-1.58). The long allele was associated with nonsevere (OR, 1.35; 95% CI, 1.07-1.70) and late-onset (OR, 1.21; 95% CI, 1.03-1.42) preeclampsia and with preeclampsia without a small-for-gestational-age infant (OR, 1.19; 95% CI, 1.02-1.40). Moreover, both the LL genotype and the long allele were associated with preeclampsia in women who had smoked during pregnancy. In conclusion, the GTn long allele seems to predispose to late-onset, less severe form of preeclampsia. This finding supports the role of HO-1 in the pathogenesis of preeclampsia and suggests that the HO-1 pathway may provide a potential target for the treatment of preeclampsia.

  3. Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

    USGS Publications Warehouse

    King, Timothy L.; Eackles, Michael S.; Reshetnikov, Andrey N.

    2015-01-01

    Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated

  4. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci.

    PubMed

    Liu, Z H; Anderson, J A; Hu, J; Friesen, T L; Rasmussen, J B; Faris, J D

    2005-08-01

    Efficient user-friendly methods for mapping plant genomes are highly desirable for the identification of quantitative trait loci (QTLs), genotypic profiling, genomic studies, and marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. Target region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects a large number of loci from a single reaction without extensive pre-PCR processing of samples. In the investigation reported here, we used both SSRs and TRAPs to generate over 700 markers for the construction of a genetic linkage map in a hard red spring wheat intervarietal recombinant inbred population. A framework map consisting of 352 markers accounted for 3,045 cM with an average density of one marker per 8.7 cM. On average, SSRs detected 1.9 polymorphic loci per reaction, while TRAPs detected 24. Both marker systems were suitable for assigning linkage groups to chromosomes using wheat aneuploid stocks. We demonstrated the utility of the maps by identifying major QTLs for days to heading and reduced plant height on chromosomes 5A and 4B, respectively. Our results indicate that TRAPs are highly efficient for genetic mapping in wheat. The maps developed will be useful for the identification of quality and disease resistance QTLs that segregate in this population.

  5. Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa

    PubMed Central

    2014-01-01

    Background Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. Findings Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. Conclusions These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species. PMID:24755442

  6. A single nucleotide polymorphism assay for the identification of unisexual Ambystoma salamanders.

    PubMed

    Greenwald, Katherine R; Lisle Gibbs, H

    2012-03-01

    Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N-5N) that reproduce via a unique system of 'leaky' gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue-spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome-related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species-specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.

  7. Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure.

    PubMed

    Bradbury, Ian R; Hamilton, Lorraine C; Dempson, Brian; Robertson, Martha J; Bourret, Vincent; Bernatchez, Louis; Verspoor, Eric

    2015-10-01

    Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

  8. Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus.

    PubMed

    Costa, Jean-Marc; Garcia-Hermoso, Dea; Olivi, Martine; Cabaret, Odile; Farrugia, Cécile; Lecellier, Gaël; Dromer, Françoise; Bretagne, Stéphane

    2010-03-01

    Microsatellite length polymorphism (MLP) typing is a PCR-based method used for genotyping of the diploid yeast Candida albicans. However, MLP is subject to homoplasia which can hamper the accuracy of the results. We combined fragment length analysis, high-resolution DNA melting (HRM) analysis, and SNaPshot minisequencing after a single amplification of the CDC3 locus to study 95 epidemiologically independent C. albicans isolates. HRM analysis for a given electrophoretic group led to a maximum of three different curves due to the presence of a SNP upstream of the tandem repeat which could be characterized using the SNaPshot assay. The combination of the three methods had a discriminatory index of 0.88 in complete congruence with previous MLP typing (Mantel test R=0.99, P<10(-)(4)). HRM is a useful tool of adding resolving power to MLP genotyping in identifying SNPs.

  9. Development of Nuclear Microsatellite Loci and Mitochondrial Single Nucleotide Polymorphisms for the Natterjack Toad, Bufo (Epidalea) calamita (Bufonidae), Using Next Generation Sequencing and Competitive Allele Specific PCR (KASPar).

    PubMed

    Faucher, Leslie; Godé, Cécile; Arnaud, Jean-François

    2016-01-01

    Amphibians are undergoing a major decline worldwide and the steady increase in the number of threatened species in this particular taxa highlights the need for conservation genetics studies using high-quality molecular markers. The natterjack toad, Bufo (Epidalea) calamita, is a vulnerable pioneering species confined to specialized habitats in Western Europe. To provide efficient and cost-effective genetic resources for conservation biologists, we developed and characterized 22 new nuclear microsatellite markers using next-generation sequencing. We also used sequence data acquired from Sanger sequencing to develop the first mitochondrial markers for KASPar assay genotyping. Genetic polymorphism was then analyzed for 95 toads sampled from 5 populations in France. For polymorphic microsatellite loci, number of alleles and expected heterozygosity ranged from 2 to 14 and from 0.035 to 0.720, respectively. No significant departures from panmixia were observed (mean multilocus F IS = -0.015) and population differentiation was substantial (mean multilocus F ST = 0.222, P < 0.001). From a set of 18 mitochondrial SNPs located in the 16S and D-loop region, we further developed a fast and cost-effective SNP genotyping method based on competitive allele-specific PCR amplification (KASPar). The combination of allelic states for these mitochondrial DNA SNP markers yielded 10 different haplotypes, ranging from 2 to 5 within populations. Populations were highly differentiated (G ST = 0.407, P < 0.001). These new genetic resources will facilitate future parentage, population genetics and phylogeographical studies and will be useful for both evolutionary and conservation concerns, especially for the set-up of management strategies and the definition of distinct evolutionary significant units.

  10. Isolation, characterization and cross-amplification of polymorphic microsatellite loci in the threatened endemic Mammillaria crucigera (Cactaceae).

    PubMed

    Solórzano, Sofia; Cortés-Palomec, Aurea C; Ibarra, Arturo; Dávila, Patricia; Oyama, Ken

    2009-01-01

    The cactus Mammillaria crucigera is a threatened species endemic to central Mexico. As a means of assessing population genetic status of these species, eight microsatellite markers were developed. These primers were tested in 40 individual from two wild populations. The results showed that these primers will be useful to describe population structure and aid to the conservation of species. The eight primers were tested in other Mammillaria species and most of them showed successful amplification.

  11. A polymorphic microsatellite repeat within the ECE-1c promoter is involved in transcriptional start site determination, human evolution, and Alzheimer's disease.

    PubMed

    Li, Yaosi; Seidel, Kerstin; Marschall, Peter; Klein, Michael; Hope, Antonia; Schacherl, Jens; Schmitz, Jennifer; Menk, Mario; Schefe, Jan H; Reinemund, Jana; Hugel, Rebecca; Walden, Peter; Schlosser, Andreas; Volkmer, Rudolf; Schimkus, Julia; Kölsch, Heike; Maier, Wolfgang; Kornhuber, Johannes; Frölich, Lutz; Klare, Sabrina; Kirsch, Sebastian; Schmerbach, Kristin; Scheele, Sylvia; Grittner, Ulrike; Zollmann, Frank; Goldin-Lang, Petra; Peters, Oliver; Kintscher, Ulrich; Unger, Thomas; Funke-Kaiser, Heiko

    2012-11-21

    Genetic factors strongly contribute to the pathogenesis of sporadic Alzheimer's disease (AD). Nevertheless, genome-wide association studies only yielded single nucleotide polymorphism loci of moderate importance. In contrast, microsatellite repeats are functionally less characterized structures within our genomes. Previous work has shown that endothelin-converting enzyme-1 (ECE-1) is able to reduce amyloid β content. Here we demonstrate that a CpG-CA repeat within the human ECE-1c promoter is highly polymorphic, harbors transcriptional start sites, is able to recruit the transcription factors poly(ADP-ribose) polymerase-1 and splicing factor proline and glutamine-rich, and is functional regarding haplotype-specific promoter activity. Furthermore, genotyping of 403 AD patients and 444 controls for CpG-CA repeat length indicated shifted allelic frequency distributions. Sequencing of 245 haplotype clones demonstrated that the overall CpG-CA repeat composition of AD patients and controls is distinct. Finally, we show that human and chimpanzee [CpG](m)-[CA](n) ECE-1c promoter repeats are genetically and functionally distinct. Our data indicate that a short genomic repeat structure constitutes a novel core promoter element, coincides with human evolution, and contributes to the pathogenesis of AD.

  12. PERMANENT GENETIC RESOURCES: Development of polymorphic microsatellite loci for the common vampire bat, Desmodus rotundus (Chiroptera: Phylostomidae).

    PubMed

    Piaggio, Antoinette J; Johnston, John J; Perkins, Susan L

    2008-03-01

    The common vampire bat (Desmodus rotundus) is one of three haematophagous species of bats and the only species in this genus. These New World bats prey on mammals and create significant economic impacts through transmission of rabies in areas where livestock are prevalent. Furthermore, in some portions of their range, it is not uncommon for them to prey upon humans. It is critical to the management of this species and for understanding the spread of bat rabies that detailed studies of D. rotundus population structure be conducted. To further such studies, we have characterized 12 microsatellite loci for this species.

  13. Linkage of morbid obesity with polymorphic microsatellite markers on chromosome 1q31 in a three-generation Canadian kindred

    SciTech Connect

    Murray, J.D.; Bulman, D.E.; Ebers, G.C. |

    1994-09-01

    Obesity is the most common nutritional disorder affecting Western societies. An estimated 3.7 million Canadians are considered to be overweight, a condition associated with hypertension, accelerated atherosclerosis, diabetes and a host of other medical problems. We have identified a 3 generation kindred in which morbid obesity appears to segregate in an autosomal dominant manner. All individuals were examined. Mass (kg) and heights (m) were measured in order to determine a body mass index (BMI) for each individual. Those individuals with BMI of greater than or equal to 30.0 were designated as affected. In the pedigree studied 25 individuals met this criteria and 12 of these were morbidly obese (BMI greater or equal to 40.0). A search of candidate genes proved unfruitful. A linkage study was initiated. All individuals in the pedigree were genotyped for microsatellite markers which were spaced every 20 centimorgans (cM). Positive evidence of linkage was detected with markers which map to 1q31-32 (lod score of 3.6 at {theta} = 0.05). Notably, strong effects for fatness in pigs have been found on pig chromosome 4 which has synteny with human chromosome 1q21-32. We are currently attempting to refine the position of this gene using linkage analysis with other microsatellite markers from this region of the genome. In addition we are screening other families in which obesity segregates for linkage to 1q31.

  14. Blueberry Microsatellite Markers Identify Cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six blueberry simple sequence repeat (SSR) markers or microsatellites were tested for the ability to amplify a polymorphic marker in eight American cranberry accessions. Sixteen SSRs resulted in informative and polymorphic SSR primer pairs and were used to fingerprint 16 economically important...

  15. Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA.

    PubMed

    Mesnick, Sarah L; Taylor, Barbara L; Archer, Frederick I; Martien, Karen K; Treviño, Sergio Escorza; Hancock-Hanser, Brittany L; Moreno Medina, Sandra Carolina; Pease, Victoria L; Robertson, Kelly M; Straley, Janice M; Baird, Robin W; Calambokidis, John; Schorr, Gregory S; Wade, Paul; Burkanov, Vladimir; Lunsford, Chris R; Rendell, Luke; Morin, Phillip A

    2011-03-01

    We use mitochondrial DNA (mtDNA) (400 bp), six microsatellites and 36 single-nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern because of both historical and contemporary impacts. We estimate genetic differentiation among three strata in the temperate to tropical waters where females are found: California Current, Hawai`i and the eastern tropical Pacific. We then consider how males on sub-Arctic foraging grounds assign to these strata. The California Current stratum was differentiated from both the other strata (P < 0.05) for mtDNA, microsatellites and SNPs, suggesting that the region supports a demographically independent population and providing the first indication that males may exhibit reproductive philopatry. Comparisons between the Hawai`i stratum and the eastern tropical Pacific stratum are not conclusive at this time. Comparisons with Alaska males were statistically significant, or nearly so, from all three strata and individuals showed mixed assignment to, and few exclusions from, the three potential source strata, suggesting widespread origin of males on sub-Arctic feeding grounds. We show that SNPs have sufficient power to detect population structure even when genetic differentiation is low. There is a need for better analytical methods for SNPs, especially when linked SNPs are used, but SNPs appear to be a valuable marker for long-term studies of globally dispersed and highly mobile species.

  16. Evaluation of anonymous and expressed sequence tag derived polymorphic microsatellite markers in the tobacco budworm Heliothis virescens (Lepidoptera: noctuidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polymorphic genetic markers were identified and characterized using a partial genomic library of Heliothis virescens enriched for simple sequence repeats (SSR) and nucleotide sequences of expressed sequence tags (EST). Nucleotide sequences of 192 clones from the partial genomic library yielded 147 u...

  17. Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus).

    PubMed Central

    Ludwig, A; Belfiore, N M; Pitra, C; Svirsky, V; Jenneckens, I

    2001-01-01

    Sturgeon (order Acipenserformes) provide an ideal taxonomic context for examination of genome duplication events. Multiple levels of ploidy exist among these fish. In a novel microsatellite approach, data from 962 fish from 20 sturgeon species were used for analysis of ploidy in sturgeon. Allele numbers in a sample of individuals were assessed at six microsatellite loci. Species with approximately 120 chromosomes are classified as functional diploid species, species with approximately 250 chromosomes as functional tetraploid species, and with approximately 500 chromosomes as functional octaploids. A molecular phylogeny of the sturgeon was determined on the basis of sequences of the entire mitochondrial cytochrome b gene. By mapping the estimated levels of ploidy on this proposed phylogeny we demonstrate that (I) polyploidization events independently occurred in the acipenseriform radiation; (II) the process of functional genome reduction is nearly finished in species with approximately 120 chromosomes and more active in species with approximately 250 chromosomes and approximately 500 chromosomes; and (III) species with approximately 250 and approximately 500 chromosomes arose more recently than those with approximately 120 chromosomes. These results suggest that gene silencing, chromosomal rearrangements, and transposition events played an important role in the acipenseriform genome formation. Furthermore, this phylogeny is broadly consistent with previous hypotheses but reveals a highly supported oceanic (Atlantic-Pacific) subdivision within the Acipenser/Huso complex. PMID:11454768

  18. Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus

    USGS Publications Warehouse

    Sonsthagen, S.A.; Sage, G.K.; Fowler, M.; Hope, A.G.; Cook, J.A.; Talbot, S.L.

    2013-01-01

    We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.

  19. POLYMORPHIC CHLOROPLAST MICROSATELLITE MARKERS IN THE OCTOPLOID LEPIDIUM MEYENII (BRASSICACEAE) AND CROSS-SPECIES AMPLIFICATION IN LEPIDIUM

    PubMed Central

    Hasan, Nabeeh A.; Mummenhoff, Klaus; Quiros, Carlos F.; Tay, C. David; Bailey, C. Donovan

    2013-01-01

    Premise of the study As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. Methods and Results Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. Conclusions These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa. PMID:21616787

  20. The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus.

    PubMed

    Miller, Adam D; Van Rooyen, Anthony; Sweeney, Oisín F; Whiterod, Nick S; Weeks, Andrew R

    2013-07-01

    The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E

  1. Cross-species amplification and polymorphism of microsatellite loci in Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) in Brazilian cropping systems.

    PubMed

    Leite, N A; Corrêa, A S; Alves-Pereira, A; Campos, J B; Zucchi, M I; Omoto, C

    2016-04-04

    The Old World bollworm Helicoverpa armigera (Hübner) was recently discovered in Brazil. This species is closely related to the New World bollworm H. zea (Boddie), and mating between these species has already been reported under laboratory conditions. Here, we tested the cross-species amplification of 20 microsatellite (SSR) loci in field populations of H. armigera and H. zea collected from Brazilian cropping systems. Seven SSR loci were successfully amplified and polymorphic in both species except for the locus HaC14, which was monomorphic for H. zea. All SSR loci were in linkage equilibrium, and deviations from Hardy- Weinberg equilibrium were only observed for the locus HarSSR1 in the HaRS-2 population, where null alleles were present. A moderate level of polymorphism was detected in H. armigera and H. zea populations with a mean allele number of 4.14, and 2.24, respectively. Interestingly, most of the populations of the recent invader H. armigera showed higher genetic diversity and inbreeding coefficients than H. zea populations. The genetic identity of each species was recovered using a STRUCTURE analysis, where the populations formed two clusters (K = 2) according to their species. STRUCTURE also suggested the occurrence of potential hybrid offspring between H. armigera and H. zea individuals in natural conditions. These SSR loci will be valuable in characterizing population differentiation, invasion routes, adaptation, reproductive behavior, and intra- and interspecific gene flow in H. armigera and H. zea populations in Brazil, the USA, and other areas where these two pests occur.

  2. [Polymorphism of Y-chromosomal microsatellites in Russian populations from the northern and southern Russia as exemplified by the populations of Kursk and Arkhangel'sk Oblast].

    PubMed

    Khrunin, A V; Bebiakova, N A; Ivanov, V P; Solodilova, M A; Limborskaia, S A

    2005-08-01

    Allelic polymorphisms at five Y-chromosomal microsatellite loci (DYS19, DYS390, DYS391, DYS392, and DYS393) were typed in 87 individuals from male population samples from two geographically isolated regions (Arkhangelsk oblast and Kursk oblast) of the European part of Russia. The populations examined demonstrated substantial differences in the distribution of the DYS392 (P = 0.005) and DYS393 (P = 0.003) alleles. Estimates of genetic relationships between these populations and some other European populations (including Eastern-Slavic) showed that irrespectively of the measure of genetic distance chosen, Arkhangelsk population was closer to the populations belonging to the Finno-Ugric linguistic group (Saami and Estonians) and to the Estonian geographical neighbors, Latvians, while Kursk population was the member of a cluster formed by Eastern-Slavic populations (Russians of Novgorod oblast, Ukrainians, and Belarussians). Phylogenetic analysis of the most frequent haplotypes indicated that these differences between Kursk and Arkhangelsk populations were associated with high prevalence in the latter of major haplotypes characteristic primarily of the Finno-Ugric populations.

  3. Linkage disequilibrium between alleles at highly polymorphic mini- and micro-satellite loci of Theileria parva isolated from cattle in three regions of Kenya.

    PubMed

    Odongo, D O; Oura, C A L; Spooner, P R; Kiara, H; Mburu, D; Hanotte, O H; Bishop, R P

    2006-07-01

    Theileria parva schizont-infected lymphocyte culture isolates from western, central and coastal Kenya were analysed for size polymorphism at 30 T. parva-specific variable number tandem repeat (VNTR) loci using a panel of mini- and micro-satellite markers. The mean number of alleles ranged from 3 to 11 at individual loci and 183 distinct alleles were observed in total, indicating high genetic diversity within the T. parva gene pool in Kenyan cattle. The frequency distribution of the length variation of specific alleles among isolates ranged from normal to markedly discontinuous. Genetic relationships between isolates were analysed using standard indices of genetic distance. Genetic distances and dendrograms derived from these using neighbour-joining algorithms did not indicate significant clustering on a geographical basis. Analysis of molecular variance demonstrated that the genetic variation between individual isolates was 72%, but only 2.3% when isolates from different regions were pooled. Both these observations suggest minimal genetic sub-structuring relative to geographical origin. Linkage disequilibrium was observed between pairs of loci within populations, as in certain Ugandan T. parva populations. A novel observation was that disequilibrium was also detected between alleles at three individual pairs of VNTR loci when isolates from the three regional meta-populations were pooled for analysis.

  4. Development and characterization of 17 polymorphic microsatellite loci in the faucet snail, Bithynia tentaculata (Gastroposa: Caenogastropoda; Bithyniidae)

    USGS Publications Warehouse

    Henningsen, Justin P.; Lance, Stacey L.; Jones, Kenneth L.; Hagen, Chris; Laurila, Joshua; Cole, Rebecca A.; Perez, Kathryn E.

    2010-01-01

    Bithynia tentaculata (Linnaeus, 1758), a snail native to Europe, was introduced into the US Great Lakes in the 1870's and has spread to rivers throughout the Northeastern US and Upper Mississippi River (UMR). Trematode parasites, for which B. tentaculata is a host, have also been introduced and are causing widespread waterfowl mortality in the UMR. Waterfowl mortality is caused by ingestion of trematode-infected B. tentaculata or insects infected with parasites released from the snails. We isolated and characterized 17 microsatellite loci from the invasive faucet snail, B. tentaculata (Gastropoda: Caenogastropoda: Bithyniidae). Loci were screened in 24 individuals of B. tentaculata. The number of alleles per locus ranged from 2 to 6, observed heterozygosity ranged from 0.050 to 0.783, and the probability of identity values ranged from 0.10 to 0.91. These new loci provide tools for examining the origin and spread of invasive populations in the US and management activities to prevent waterfowl mortality.

  5. Microsatellite analysis of malaria parasites.

    PubMed

    Orjuela-Sánchez, Pamela; Brandi, Michelle C; Ferreira, Marcelo U

    2013-01-01

    Microsatellites have been increasingly used to investigate the population structure of malaria parasites, to map genetic loci contributing to phenotypes such as drug resistance and virulence in laboratory crosses and genome-wide association studies and to distinguish between treatment failures and new infections in clinical trials. Here, we provide optimized protocols for genotyping highly polymorphic microsatellites sampled from across the genomes of the human malaria parasites Plasmodium falciparum and P. vivax that have been extensively used in research laboratories worldwide.

  6. Transpecific microsatellites for hard pines.

    PubMed

    Shepherd, M.; Cross, M.; Maguire, L.; Dieters, J.; Williams, G.; Henry, J.

    2002-04-01

    Microsatellites are difficult to recover from large plant genomes so cross-specific utilisation is an important source of markers. Fifty microsatellites were tested for cross-specific amplification and polymorphism to two New World hard pine species, slash pine ( Pinus elliottii var. elliottii) and Caribbean pine ( P. caribaea var. hondurensis). Twenty-nine (58%) markers amplified in both hard pine species, and 23 of these 29 were polymorphic. Soft pine (subgenus Strobus) microsatellite markers did amplify, but none were polymorphic. Pinus elliottii var. elliottii and P. caribaea var. hondurensis showed mutational changes in the flanking regions and the repeat motif that were informative for Pinus spp. phylogenetic relationships. Most allele length variation could be attributed to variability in repeat unit number. There was no evidence for ascertainment bias.

  7. Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus.

    PubMed

    Silvestrini, Milene; Pinto-Maglio, Cecília A F; Zucchi, Maria I; dos Santos, Flavio A M

    2013-12-01

    Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.

  8. Effect of oral N-acetylcysteine on COPD patients with microsatellite polymorphism in the heme oxygenase-1 gene promoter

    PubMed Central

    Zhang, Jia-Qiang; Zhang, Jian-Qing; Fang, Li-Zhou; Liu, Ling; Fu, Wei-Ping; Dai, Lu-Ming

    2015-01-01

    Background Heme oxygenase-1 (HO-1) plays a protective role as an antioxidant in the lung, and HO-1 gene promoter polymorphism has been shown to be associated with the severity and prognosis of COPD patients. N-acetylcysteine (NAC), an antioxidant/mucous modifier, has shown an uncertain benefit in COPD patients. We hypothesized that this polymorphism could be associated with the effectiveness of oral NAC. Methods A total of 368 patients with COPD were recruited and the polymorphisms of their HO-1 gene promoter were classified into three subclasses according to the number of (GT)n repeats, as previously reported: class S (<27 (GT)n repeats), class M (27–32 (GT)n repeats), and class L (>32 (GT)n repeats). These subjects were then classified as L+ group (with the L allele: L/L, L/M, L/S) and L− group (without the L allele: M/M, M/S, S/S). All the patients were allocated to standard therapy plus NAC 600 mg bid over a 1-year period and were observed over that year. Results The L− group saw improvements in forced expiratory volume in 1 second (FEV1) (from 1.44±0.37 to 1.58±0.38, P=0.04) and FEV1% predicted (from 56.6±19.2 to 59.7±17.2, P=0.03). No improvement was found in forced vital capacity of each group and the decline of forced vital capacity in both of the groups was not statistical significant. The number of yearly COPD exacerbations of the L− group was 1.5±0.66 which was lower than the 2.1±0.53 of the L+ group (P<0.01). For the changes of St George’s Respiratory Questionnaire (SGRQ) score, only the activity score of the L− group was more significant than that of the L+ group (P=0.02). The improvement of the outcome of 6-minute walking distance test in L− group (from 290.1±44.9 meters to 309.7±46.9 m) was higher than that in the L+ group (from 289.7±46.2 m to 300.3±44.2 m) (P=0.03). Conclusion A 600 mg bid oral NAC treatment for 1-year on COPD patients without the L allele can improve the FEV1, FEV1% predicted, the SGRQ activity score, and

  9. New polymorphic microsatellite markers derived from hemocyte cDNA library of Manila clam Ruditapes philippinarum challenged by the protozoan parasite Perkinsus olseni

    NASA Astrophysics Data System (ADS)

    Kang, Hyun-Sil; Hong, Hyun-Ki; Park, Kyung-Il; Cho, Moonjae; Youn, Seok-Hyun; Choi, Kwang-Sik

    2017-02-01

    Manila clam Ruditapes philippinarum is one of the most important benthic animals in the coastal north Pacific region, where clam populations have been mixed genetically through trade and aquaculture activities. Accordingly, identification of the genetically different clam populations has become one of the most important issues to manage interbreeding of the local and introduced clam populations. To identify genetically different populations of clam populations, we developed 11 expressed sequence tag (EST)-microsatellite loci (i.e., simple sequence repeat, SSR) from 1,128 clam hemocyte cDNA clones challenged by the protozoan parasite Perkinsus olseni. Genotype analysis using the markers developed in this study demonstrated that clams from a tidal flat on the west coast contained 6 to 19 alleles per locus, and a population from Jeju Island had 4 to 20 alleles per locus. The expected heterozygosity of the 2 clam populations ranged from 0.472 to 0.919 for clams from the west coast, and 0.494 to 0.919 for clams from Jeju Island, respectively. Among the 11 loci discovered in this study, 7 loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction. The 5 loci developed in this study also successfully amplified the SSRs of R. variegatus, a clam species taxonomically very close to R. philippinarum, from Hong Kong and Jeju Island. We believe that the 11 novel polymorphic SSR developed in this study can be utilized successfully in Manila clam genetic diversity analysis, as well as in genetic discrimination of different clam populations.

  10. New polymorphic microsatellite markers derived from hemocyte cDNA library of Manila clam Ruditapes philippinarum challenged by the protozoan parasite Perkinsus olseni

    NASA Astrophysics Data System (ADS)

    Kang, Hyun-Sil; Hong, Hyun-Ki; Park, Kyung-Il; Cho, Moonjae; Youn, Seok-Hyun; Choi, Kwang-Sik

    2017-03-01

    Manila clam Ruditapes philippinarum is one of the most important benthic animals in the coastal north Pacific region, where clam populations have been mixed genetically through trade and aquaculture activities. Accordingly, identification of the genetically different clam populations has become one of the most important issues to manage interbreeding of the local and introduced clam populations. To identify genetically different populations of clam populations, we developed 11 expressed sequence tag (EST)-microsatellite loci (i.e., simple sequence repeat, SSR) from 1,128 clam hemocyte cDNA clones challenged by the protozoan parasite Perkinsus olseni. Genotype analysis using the markers developed in this study demonstrated that clams from a tidal flat on the west coast contained 6 to 19 alleles per locus, and a population from Jeju Island had 4 to 20 alleles per locus. The expected heterozygosity of the 2 clam populations ranged from 0.472 to 0.919 for clams from the west coast, and 0.494 to 0.919 for clams from Jeju Island, respectively. Among the 11 loci discovered in this study, 7 loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction. The 5 loci developed in this study also successfully amplified the SSRs of R. variegatus, a clam species taxonomically very close to R. philippinarum, from Hong Kong and Jeju Island. We believe that the 11 novel polymorphic SSR developed in this study can be utilized successfully in Manila clam genetic diversity analysis, as well as in genetic discrimination of different clam populations.

  11. Genetic diversity of Histoplasma capsulatum isolated from infected bats randomly captured in Mexico, Brazil, and Argentina, using the polymorphism of (GA)(n) microsatellite and its flanking regions.

    PubMed

    Taylor, Maria Lucia; Hernández-García, Lorena; Estrada-Bárcenas, Daniel; Salas-Lizana, Rodolfo; Zancopé-Oliveira, Rosely M; García de la Cruz, Saúl; Galvão-Dias, Maria A; Curiel-Quesada, Everardo; Canteros, Cristina E; Bojórquez-Torres, Georgina; Bogard-Fuentes, Carlos A; Zamora-Tehozol, Erick

    2012-02-01

    The genetic diversity of 47 Histoplasma capsulatum isolates from infected bats captured in Mexico, Brazil, and Argentina was studied, using sequence polymorphism of a 240-nucleotides (nt) fragment, which includes the (GA)(n) length microsatellite and its flanking regions within the HSP60 gene. Three human clinical strains were used as geographic references. Based on phylogenetic analyses of 240-nt fragments achieved, the relationships among H. capsulatum isolates were resolved using neighbour-joining and maximum parsimony methods. The tree topologies obtained by both methods were identical and highlighted two major clusters of isolates. Cluster I had three sub-clusters (Ia, Ib, and Ic), all of which contained Mexican H. capsulatum samples, while cluster II consisted of samples from Brazil and Argentina. Sub-cluster Ia included only fungal isolates from the migratory bat Tadarida brasiliensis. An average DNA mutation rate of 2.39 × 10(-9) substitutions per site per year was estimated for the 240-nt fragment for all H. capsulatum isolates. Nucleotide diversity analysis of the (GA)(n) and flanking regions from fungal isolates of each cluster and sub-cluster underscored the high similarity of cluster II (Brazil and Argentina), sub-clusters Ib, and Ic (Mexico). According to the genetic distances among isolates, a network of the 240-nt fragment was graphically represented by (GA)(n) length haplotype. This network showed an association between genetic variation and both the geographic distribution and the ecotype dispersion of H. capsulatum, which are related to the migratory behaviour of the infected bats studied.

  12. The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods

    PubMed Central

    Klie, Maik; Schie, Stephan; Linde, Marcus; Debener, Thomas

    2014-01-01

    Polyploidy is a widespread phenomenon among higher plants and a major factor shaping the structure and evolution of plant genomes. The important ornamental chrysanthemum (Chrysanthemum indicum hybrid) possesses a hexaploid genome with 54 chromosomes and was classified based on its evolutionary origin and cytological methods as an allopolyploid. However, it is questionable whether cytological methods are sufficient to determine the type of ploidy, and there are more informative methods available based on molecular marker analyses. Therefore, we collected segregation data for 406 dominant molecular marker alleles [327 amplified fragment length polymorphism (AFLPs), 65 single-strand conformation polymorphism (SSCPs) and 14 microsatellites (EST-SSRs)] in a biparental F1 population of 160 individuals. We analyzed these data for the characteristics that differ between allopolyploids and autopolyploids, including the segregation ratio of each marker, the ratio of single-dose (SD) to multi-dose (MD) markers, the ratio of SD markers in coupling to those in repulsion and the banding patterns of the SSRs. Whereas the analysis of the segregation ratio of each polymorphic marker indicated disomic (13 markers) as well as hexasomic (eight markers) inheritance, the ratio of SD markers in coupling to those in repulsion was 1:0, which is characteristic of autopolyploids. The observed ratio of SD to MD markers was 0.67:0.33 which is significantly different to the expected segregation for auto- and allohexaploids. Furthermore, the three EST-SSR alleles were inherited in all possible combinations and were not independent of each other, as expected for fixed heterozygosity in allopolyploids. Combining our results with published cytological data indicates that cultivated chrysanthemums should be classified as segmental allohexaploids. PMID:25295046

  13. Variation in cytosine methylation patterns during ploidy level conversions in Eragrostis curvula.

    PubMed

    Ochogavía, Ana C; Cervigni, Gerardo; Selva, Juan P; Echenique, Viviana C; Pessino, Silvina C

    2009-05-01

    In many species polyploidization involves rearrangements of the progenitor genomes, at both genetic and epigenetic levels. We analyzed the cytosine methylation status in a 'tetraploid-diploid-tetraploid' series of Eragrostis curvula with a common genetic background by using the MSAP (Methylation-sensitive Amplified Polymorphism) technique. Considerable levels of polymorphisms were detected during ploidy conversions. The total level of methylation observed was lower in the diploid genotype compared to the tetraploid ones. A significant proportion of the epigenetic modifications occurring during the tetraploid-diploid conversion reverted during the diploid-tetraploid one. Genetic and expression data from previous work were used to analyze correlation with methylation variation. All genetic, epigenetic and gene expression variation data correlated significantly when compared by pairs in simple Mantel tests. Dendrograms reflecting genetic, epigenetic and expression distances as well as principal coordinate analysis suggested that plants of identical ploidy levels present similar sets of data. Twelve (12) different genomic fragments displaying different methylation behavior during the ploidy conversions were isolated, sequenced and characterized.

  14. Microsatellite development and flow cytometry in the African tree genus Afzelia (Fabaceae, Caesalpinioideae) reveal a polyploid complex1

    PubMed Central

    Donkpegan, Armel S. L.; Doucet, Jean-Louis; Dainou, Kasso; Hardy, Olivier J.

    2015-01-01

    • Premise of the study: Microsatellites were developed in the vulnerable African rainforest tree Afzelia bipindensis to investigate gene flow patterns. • Methods and Results: Using 454 GS-FLX technique, 16 primer sets were identified and optimized, leading to 11 polymorphic and readable markers displaying each six to 25 alleles in a population. Up to four alleles per individual were found in each of the loci, without evidence of fixed heterozygosity, suggesting an autotetraploid genome. Cross-amplification succeeded for all loci in the African rainforest species A. pachyloba and A. bella, which appeared tetraploid, and for most loci in the African woodland species A. africana and A. quanzensis, which appeared diploid, but failed in the Asian species A. xylocarpa. Flow cytometry confirmed the suspected differences in ploidy. • Conclusions: African Afzelia species are diploid or tetraploid, a situation rarely documented in tropical trees. These newly developed microsatellites will help in the study of their mating system and gene flow patterns. PMID:25606356

  15. Comparison of SNPs and microsatellites in identifying offtypes of cacao clones from Cameroon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single Nucleotide Polymorphism (SNP) markers are increasingly being used in crop breeding programs, slowly replacing microsatellites and other markers. SNPs provide many benefits over microsatellites, including ease of analysis and unambiguous results across various platforms. We compare SNPs to m...

  16. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species

    PubMed Central

    2013-01-01

    Background Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient “off-the-shelf” markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions When combined with previously described conserved loci, this new set of conserved markers will not only

  17. Distant hybridization leads to different ploidy fishes.

    PubMed

    Liu, ShaoJun

    2010-04-01

    Distant hybridization makes it possible to transfer the genome of one species to another, which results in changes in phenotypes and genotypes of the progenies. This study shows that distant hybridization or the combination of this method with gynogenesis or androgenesis lead to different ploidy fishes with genetic variation, including fertile tetraploid hybrids, sterile triploid hybrids, fertile diploid hybrids, fertile diploid gynogenetic fish, and their derived progenies. The formations of the different ploidy fishes depend on the genetic relationship between the parents. In this study, several types of distant hybridization, including red crucian carp (Carassius auratus red var.) (2n=100, abbreviated as RCC) (female) x common carp (Cyprinus carpio L.) (2n=100, abbreviated as CC) (male), and RCC (2n=100) (female) x blunt snout bream (Megalobrama amblycephala) (2n=48, abbreviated as BSB) (male) are described. In the distant hybridization of RCC (female) x CC (male), bisexual fertile F(3)-F(18) allotetraploid hybrids (4n=200, abbreviated as 4nAT) were formed. The diploid hybrid eggs and diploid sperm generated by the females and males of 4nAT developed into diploid gynogenetic hybrids and diploid androgenetic hybrids, respectively, by gynogenesis and androgenesis, without treatment for doubling the chromosome. Improved tetraploid hybrids and improved diploid fishes with genetic variation were derived from the gynogenetic hybrid line. The improved diploid fishes included the high-body RCC and high-body goldfish. The formation of the tetraploid hybrids was related to the occurrence of unreduced gametes generated from the diploid hybrids, which involved in premeiotic endoreduplication, endomitosis, or fusion of germ cells. The sterile triploid hybrids (3n=150) were produced on a large scale by crossing the males of tetraploid hybrids with females of diploid fish (2n=100). In another distant hybridization of RCC (female) x BSB (male), different ploidy fishes were

  18. Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen.

    PubMed

    Gerstein, Aleeza C; Lim, Heekyung; Berman, Judith; Hickman, Meleah A

    2017-04-01

    Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term "ploidy drive." We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged toward diploidy (the baseline ploidy of C. albicans). Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.

  19. Microsatellite characterization of Cimarron Uruguayo dogs

    PubMed Central

    Gagliardi, Rosa; Llambí, Silvia; García, Cristina; Arruga, María Victoria

    2011-01-01

    Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity. PMID:21637561

  20. Triplet-repeat microsatellites shared among hard and soft pines.

    PubMed

    Kutil, B L; Williams, C G

    2001-01-01

    Vascular plant species have shown a low level of microsatellite conservation compared to many animal species. Finding trans-specific microsatellites for plants may be improved by using a priori knowledge of genome organization. Fifteen triplet-repeat microsatellites from hard pine (Pinus taeda L.) were tested for trans-specific amplification across seven hard pines (P. palustris Mill., P. echinata Mill., P. radiata D. Don., P. patula Schiede et Deppe, P. halepensis Mill., P. kesiya Royle), a soft pine (P. strobus L.), and Picea rubens Sargent. Seven of 15 microsatellites had trans-specific amplification in both hard and soft pine subgenera. Two P. taeda microsatellites had conserved flanking regions and repeat motifs in all seven hard pines, soft pine P. strobus, and P. rubens. Perfect triplet-repeat P. taeda microsatellites appear to be better candidates for trans-specific polymorphism than compound microsatellites. Not all perfect triplet-repeat microsatellites were conserved, but all conserved microsatellites had perfect repeat motifs. Persistent microsatellites PtTX2123 and PtTX3020 had highly conserved flanking regions and a conserved repeat motif composition with variable repeat unit numbers. Using trinucleotide microsatellites improved trans-specific microsatellite recovery among hard and soft pine species.

  1. Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Microsatellite loci were developed for Cornus sanguinea and will permit genetic and conservation studies of the species. Methods and Results: A microsatellite-enriched library was used to develop 16 polymorphic microsatellite loci for C. sanguinea. The loci amplified 5-11 allel...

  2. Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. Methods and Results:A microsatellite enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci ...

  3. Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22.

    PubMed

    Middleton, F A; Pato, M T; Gentile, K L; Morley, C P; Zhao, X; Eisener, A F; Brown, A; Petryshen, T L; Kirby, A N; Medeiros, H; Carvalho, C; Macedo, A; Dourado, A; Coelho, I; Valente, J; Soares, M J; Ferreira, C P; Lei, M; Azevedo, M H; Kennedy, J L; Daly, M J; Sklar, P; Pato, C N

    2004-05-01

    We performed a linkage analysis on 25 extended multiplex Portuguese families segregating for bipolar disorder, by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay, the GeneChip Human Mapping 10K Array (HMA10K). Of these families, 12 were used for a direct comparison of the HMA10K with the traditional 10-cM microsatellite marker set and the more dense 4-cM marker set. This comparative analysis indicated the presence of significant linkage peaks in the SNP assay in chromosomal regions characterized by poor coverage and low information content on the microsatellite assays. The HMA10K provided consistently high information and enhanced coverage throughout these regions. Across the entire genome, the HMA10K had an average information content of 0.842 with 0.21-Mb intermarker spacing. In the 12-family set, the HMA10K-based analysis detected two chromosomal regions with genomewide significant linkage on chromosomes 6q22 and 11p11; both regions had failed to meet this strict threshold with the microsatellite assays. The full 25-family collection further strengthened the findings on chromosome 6q22, achieving genomewide significance with a maximum nonparametric linkage (NPL) score of 4.20 and a maximum LOD score of 3.56 at position 125.8 Mb. In addition to this highly significant finding, several other regions of suggestive linkage have also been identified in the 25-family data set, including two regions on chromosome 2 (57 Mb, NPL = 2.98; 145 Mb, NPL = 3.09), as well as regions on chromosomes 4 (91 Mb, NPL = 2.97), 16 (20 Mb, NPL = 2.89), and 20 (60 Mb, NPL = 2.99). We conclude that at least some of the linkage peaks we have identified may have been largely undetected in previous whole-genome scans for bipolar disorder because of insufficient coverage or information content, particularly on chromosomes 6q22 and 11p11.

  4. Genomewide Linkage Analysis of Bipolar Disorder by Use of a High-Density Single-Nucleotide–Polymorphism (SNP) Genotyping Assay: A Comparison with Microsatellite Marker Assays and Finding of Significant Linkage to Chromosome 6q22

    PubMed Central

    Middleton, F. A.; Pato, M. T.; Gentile, K. L.; Morley, C. P.; Zhao, X.; Eisener, A. F.; Brown, A.; Petryshen, T. L.; Kirby, A. N.; Medeiros, H.; Carvalho, C.; Macedo, A.; Dourado, A.; Coelho, I.; Valente, J.; Soares, M. J.; Ferreira, C. P.; Lei, M.; Azevedo, M. H.; Kennedy, J. L.; Daly, M. J.; Sklar, P.; Pato, C. N.

    2004-01-01

    We performed a linkage analysis on 25 extended multiplex Portuguese families segregating for bipolar disorder, by use of a high-density single-nucleotide–polymorphism (SNP) genotyping assay, the GeneChip Human Mapping 10K Array (HMA10K). Of these families, 12 were used for a direct comparison of the HMA10K with the traditional 10-cM microsatellite marker set and the more dense 4-cM marker set. This comparative analysis indicated the presence of significant linkage peaks in the SNP assay in chromosomal regions characterized by poor coverage and low information content on the microsatellite assays. The HMA10K provided consistently high information and enhanced coverage throughout these regions. Across the entire genome, the HMA10K had an average information content of 0.842 with 0.21-Mb intermarker spacing. In the 12-family set, the HMA10K-based analysis detected two chromosomal regions with genomewide significant linkage on chromosomes 6q22 and 11p11; both regions had failed to meet this strict threshold with the microsatellite assays. The full 25-family collection further strengthened the findings on chromosome 6q22, achieving genomewide significance with a maximum nonparametric linkage (NPL) score of 4.20 and a maximum LOD score of 3.56 at position 125.8 Mb. In addition to this highly significant finding, several other regions of suggestive linkage have also been identified in the 25-family data set, including two regions on chromosome 2 (57 Mb, NPL = 2.98; 145 Mb, NPL = 3.09), as well as regions on chromosomes 4 (91 Mb, NPL = 2.97), 16 (20 Mb, NPL = 2.89), and 20 (60 Mb, NPL = 2.99). We conclude that at least some of the linkage peaks we have identified may have been largely undetected in previous whole-genome scans for bipolar disorder because of insufficient coverage or information content, particularly on chromosomes 6q22 and 11p11. PMID:15060841

  5. Microsatellite DNA capture from enriched libraries.

    PubMed

    Gonzalez, Elena G; Zardoya, Rafael

    2013-01-01

    Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

  6. Microsatellites as targets of natural selection.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2013-02-01

    The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich's ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants.

  7. Development of inhibitory antibodies to therapeutic factor VIII in severe hemophilia A is associated with microsatellite polymorphisms in the HMOX1 promoter.

    PubMed

    Repessé, Yohann; Peyron, Ivan; Dimitrov, Jordan D; Dasgupta, Suryasarathi; Moshai, Elika Farrokhi; Costa, Catherine; Borel-Derlon, Annie; Guillet, Benoit; D'Oiron, Roseline; Aouba, Achille; Rothschild, Chantal; Oldenburg, Johannes; Pavlova, Anna; Kaveri, Srinivas V; Lacroix-Desmazes, Sébastien

    2013-10-01

    Induction of heme oxygenase-1, a stress-inducible enzyme with anti-inflammatory activity, reduces the immunogenicity of therapeutic factor VIII in experimental hemophilia A. In humans, heme oxygenase-1 expression is modulated by polymorphisms in the promoter of the heme oxygenase-1-encoding gene (HMOX1). We investigated the relationship between polymorphisms in the HMOX1 promoter and factor VIII inhibitor development in severe hemophilia A. We performed a case-control study on 99 inhibitor-positive patients and 263 patients who did not develop inhibitors within the first 150 cumulative days of exposure to therapeutic factor VIII. Direct sequencing and DNA fragment analysis were used to study (GT)n polymorphism and single nucleotide polymorphisms located at -1135 and -413 in the promoter of HMOX1. We assessed associations between the individual allele frequencies or genotypes, and inhibitor development. Our results demonstrate that inhibitor-positive patients had a higher frequency of alleles with large (GT)n repeats (L: n≥30), which are associated with lesser heme oxygenase-1 expression (odds ratio 2.31; 95% confidence interval 1.46-3.66; P<0.001]. Six genotypes (L/L, L/M, L/S, M/M, M/S and S/S) of (GT)n repeats were identified (S: n<21; M: 21≤n<30). The genotype group including L alleles (L/L, L/M and L/S) was statistically more frequent among inhibitor-positive than inhibitor-negative patients, as compared to the other genotypes (33.3% versus 17.1%) (odds ratio 2.21, 95% confidence interval 1.30-3.76; P<0.01). To our knowledge, this is the first association identified between HMOX1 promoter polymorphism and development of anti-drug antibodies. Our study paves the way towards modulation of the endogenous anti-inflammatory machinery of hemophilia patients to reduce the risk of inhibitor development.

  8. Ploidy variation in multinucleate cells changes under stress

    PubMed Central

    Anderson, Cori A.; Roberts, Samantha; Zhang, Huaiying; Kelly, Courtney M.; Kendall, Alexxy; Lee, ChangHwan; Gerstenberger, John; Koenig, Aaron B.; Kabeche, Ruth; Gladfelter, Amy S.

    2015-01-01

    Ploidy variation is found in contexts as diverse as solid tumors, drug resistance in fungal infection, and normal development. Altering chromosome or genome copy number supports adaptation to fluctuating environments but is also associated with fitness defects attributed to protein imbalances. Both aneuploidy and polyploidy can arise from multinucleate states after failed cytokinesis or cell fusion. The consequences of ploidy variation in syncytia are difficult to predict because protein imbalances are theoretically buffered by a common cytoplasm. We examined ploidy in a naturally multinucleate fungus, Ashbya gossypii. Using integrated lac operator arrays, we found that chromosome number varies substantially among nuclei sharing a common cytoplasm. Populations of nuclei range from 1N to >4N, with different polyploidies in the same cell and low levels of aneuploidy. The degree of ploidy variation increases as cells age. In response to cellular stress, polyploid nuclei diminish and haploid nuclei predominate. These data suggest that mixed ploidy is tolerated in these syncytia; however, there may be costs associated with variation as stress homogenizes the genome content of nuclei. Furthermore, the results suggest that sharing of gene products is limited, and thus there is incomplete buffering of ploidy variation despite a common cytosol. PMID:25631818

  9. Molecular epidemiology and in-vitro antifungal susceptibility of Aspergillus terreus species complex isolates in Delhi, India: evidence of genetic diversity by amplified fragment length polymorphism and microsatellite typing.

    PubMed

    Kathuria, Shallu; Sharma, Cheshta; Singh, Pradeep Kumar; Agarwal, Puneet; Agarwal, Kshitij; Hagen, Ferry; Meis, Jacques F; Chowdhary, Anuradha

    2015-01-01

    Aspergillus terreus is emerging as an etiologic agent of invasive aspergillosis in immunocompromised individuals in several medical centers in the world. Infections due to A. terreus are of concern due to its resistance to amphotericin B, in vivo and in vitro, resulting in poor response to antifungal therapy and high mortality. Herein we examined a large collection of molecularly characterized, geographically diverse A. terreus isolates (n = 140) from clinical and environmental sources in India for the occurrence of cryptic A. terreus species. The population structure of the Indian A. terreus isolates and their association with those outside India was determined using microsatellite based typing (STR) technique and Amplified Fragment Length Polymorphism analysis (AFLP). Additionally, in vitro antifungal susceptibility of A. terreus isolates was determined against 7 antifungals. Sequence analyses of the calmodulin locus identified the recently described cryptic species A. hortai, comprising 1.4% of Aspergillus section Terrei isolates cultured from cases of aspergilloma and probable invasive aspergillosis not reported previously. All the nine markers used for STR typing of A. terreus species complex proved to be highly polymorphic. The presence of high genetic diversity revealing 75 distinct genotypes among 101 Indian A. terreus isolates was similar to the marked heterogeneity noticed in the 47 global A. terreus population exhibiting 38 unique genotypes mainly among isolates from North America and Europe. Also, AFLP analysis showed distinct banding patterns for genotypically diverse A. terreus isolates. Furthermore, no correlation between a particular genotype and amphotericin B susceptibility was observed. Overall, 8% of the A. terreus isolates exhibited low MICs of amphotericin B. All the echinocandins and azoles (voriconazole, posaconazole and isavuconazole) demonstrated high potency against all the isolates. The study emphasizes the need of molecular

  10. Molecular Epidemiology and In-Vitro Antifungal Susceptibility of Aspergillus terreus Species Complex Isolates in Delhi, India: Evidence of Genetic Diversity by Amplified Fragment Length Polymorphism and Microsatellite Typing

    PubMed Central

    Kathuria, Shallu; Sharma, Cheshta; Singh, Pradeep Kumar; Agarwal, Puneet; Agarwal, Kshitij; Hagen, Ferry; Meis, Jacques F.; Chowdhary, Anuradha

    2015-01-01

    Aspergillus terreus is emerging as an etiologic agent of invasive aspergillosis in immunocompromised individuals in several medical centers in the world. Infections due to A. terreus are of concern due to its resistance to amphotericin B, in vivo and in vitro, resulting in poor response to antifungal therapy and high mortality. Herein we examined a large collection of molecularly characterized, geographically diverse A. terreus isolates (n = 140) from clinical and environmental sources in India for the occurrence of cryptic A. terreus species. The population structure of the Indian A. terreus isolates and their association with those outside India was determined using microsatellite based typing (STR) technique and Amplified Fragment Length Polymorphism analysis (AFLP). Additionally, in vitro antifungal susceptibility of A. terreus isolates was determined against 7 antifungals. Sequence analyses of the calmodulin locus identified the recently described cryptic species A. hortai, comprising 1.4% of Aspergillus section Terrei isolates cultured from cases of aspergilloma and probable invasive aspergillosis not reported previously. All the nine markers used for STR typing of A. terreus species complex proved to be highly polymorphic. The presence of high genetic diversity revealing 75 distinct genotypes among 101 Indian A. terreus isolates was similar to the marked heterogeneity noticed in the 47 global A. terreus population exhibiting 38 unique genotypes mainly among isolates from North America and Europe. Also, AFLP analysis showed distinct banding patterns for genotypically diverse A. terreus isolates. Furthermore, no correlation between a particular genotype and amphotericin B susceptibility was observed. Overall, 8% of the A. terreus isolates exhibited low MICs of amphotericin B. All the echinocandins and azoles (voriconazole, posaconazole and isavuconazole) demonstrated high potency against all the isolates. The study emphasizes the need of molecular

  11. Comparison of DNA ploidy status and DNA ploidy-related parameters in malignant melanoma tissue microarrays and full sections.

    PubMed

    Korabiowska, Monika; Cordon-Cardo, Carlos; Buschmann, Nadine; Stachura, Jerzy; Fischer, Gösta; Brinck, Ulrich

    2004-07-01

    A new high-throughput tissue-arraying technique, now frequently used in tumor pathology, requires standardization of methods of DNA analysis, previously applied in full histological sections. The main objectives of this study were to evaluate DNA ploidy status and DNA ploidy-related parameters using the CAS200 image analyzer in malignant melanoma tissue microarrays and to compare them with full histological sections. Comparison of DNA ploidy-related parameters, including percentage of diploid cells, percentage of aneuploid cells between 2c and 4c, percentage of tetraploid cells, percentage of aneuploid cells between 4c and 8c, percentage of octaploid cells, percentage of 16-ploid cells, and 5c exceeding rate, did not reveal any significant differences between malignant melanoma tissue microarrays and full sections. The DNA ploidy status according to Auer differed in 1 out of 59 cases investigated. Our study demonstrated that it is possible to evaluate DNA ploidy status and DNA ploidy-related parameters in tissue microarrays, which is of practical relevance to tumor pathology.

  12. A 4. 5-megabase yeast artificial chromosome contig from human chromosome 13q14. 3 ordering 9 polymorphic microsatellites (22 sequence-tagged sites) tightly linked to the Wilson disease locus

    SciTech Connect

    White, A.; Tomfohrde, J.; Barnes, R. ); Stewart, E.; Cavalli-Sforza, L. ); Le Paslier, D. ); Weissenbach, J. ); Farrer, L. ); Bowcock, A. Eugene McDermott Center of Human Growth and Development, Dallas, TX )

    1993-11-15

    The authors have previously performed a genetic analysis of multiply affected families to map a locus responsible for Wilson disease (WND) to a 0.3-centimorgan (cM) region within chromosome 13q14.3, between D12S31 and D13S59. Here they describe the construction of a contig of [approx]4.5 Mb, which spans this region and extends from D13S25 to D13S59. This contig consists of 28 genomic yeast artificial chromosome (YAC) clones. Five critical crossover events have been defined in this interval in two unaffected (Centre d'Etudes du Polymorphisme Humain) and three WND families. The combination of sequence tagged site content mapping of YACs with both polymorphic and nonpolymorphic markers and recombination breakpoint mapping resulted in the following order of polymorphic markers: centromere-RB1-D13S25-AFM205vh2-D13S31-D13S227-D13S228-AFM238vc3-D13S133-AFM084xc5-D13S137-D13S169, D13S155-D13S59-telomere. The recombination/physical distance ratio varies from [approx] 3000 kb per cM in the region between D13S31 and D13S25 to 6000 kb per cM in the region between D13S31 and D13S59. Three WND families exhibiting recombination between the disease locus and D13S31 or D13S59 were genotyped for additional markers in this region and further refined the location of the WND gene to between D13S155 and D13S133. Nine of the markers in this region of <1 cM are polymorphic microsatellites (seven have observed heterozygosities of 70% or above) that will be extremely useful in prenatal and preclinical diagnosis of this disease. This physical map is an essential step in the isolation of the WND gene and is a framework for the identification of candidate genes.

  13. New softwares for automated microsatellite marker development

    PubMed Central

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimarães, Patrícia; Moretzsohn, Marcio; Bertioli, David

    2006-01-01

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence ‘experiment file’ format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut. PMID:16493138

  14. New softwares for automated microsatellite marker development.

    PubMed

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimarães, Patrícia; Moretzsohn, Marcio; Bertioli, David

    2006-02-21

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.

  15. Ploidy Determination in Agrostis Using Flow Cytometry and Morphological Traits.

    PubMed

    Bonos, Stacy A.; Plumley, Karen A.; Meyer, William A.

    2002-01-01

    The taxonomic classification of the genus Agrostis is one of the most complicated of the grass genera. Classification based upon morphological and anatomical characters is difficult and complicated by the presence of intermediate forms and the misapplication of names. Determining ploidy levels of new germplasm can assist in species determination and is necessary before initiating breeding or genetics studies. The objectives of this study were to (i) evaluate the use of laser flow cytometry as a quick, reliable tool to determine ploidy level and aid in Agrostis species determination, and (ii) identify morphological characters associated with DNA content or ploidy level. The six Agrostis species evaluated were A. canina L. subsp. canina, A. canina L. subsp. montana (Hartm.) Hartm., A. palustris Huds. [= A. stolonifera var. palustris (Huds.) Farw.], A. tenuis Sibth. (= A. capillaris L.), A. castellana Boiss. & Reut., and A. alba L. Ploidy level was determined by flow cytometry and root tip chromosome counts. Plant height, panicle height, flag leaf length, flag leaf width, and highest internode length of mature field-grown spaced plants were measured. Significant differences in 2C DNA content were found between species (P < 0.01) differing in ploidy level. Flow cytometry was effective in differentiating between diploid, tetraploid, and hexaploid species. Chromosome numbers previously reported and those observed in this study were positively correlated with 2C nuclear DNA content (r = 0.98, P < 0.01). Flag leaf length was the only morphological measurement taken that was significantly positively correlated to DNA content (r = 0.98, P < 0.001). The results of this study indicate that laser flow cytometry is a quick, reliable tool to determine ploidy levels and infer certain species of AGROSTIS: This technique will aid breeders to quickly and accurately determine ploidy levels of new germplasm collections.

  16. Analysis of new microsatellite markers developed from reported sequences of Japanese flounder Paralichthys olivaceus

    NASA Astrophysics Data System (ADS)

    Yu, Haiyang; Jiang, Liming; Chen, Wei; Wang, Xubo; Wang, Zhigang; Zhang, Quanqi

    2010-12-01

    The expressed sequence tags (ESTs) of Japanese flounder, Paralichthys olivaceus, were selected from GenBank to identify simple sequence repeats (SSRs) or microsatellites. A bioinformatic analysis of 11111 ESTs identified 751 SSR-containing ESTs, including 440 dinucleotide, 254 trinucleotide, 53 tetranucleotide, 95 pentanucleotide and 40 hexanucleotide microsatellites respectively. The CA/TG and GA/TC repeats were the most abundant microsatellites. AT-rich types were predominant among trinucleotide and tetranucleotide microsatellites. PCR primers were designed to amplify 10 identified microsatellites loci. The PCR results from eight pairs of primers showed polymorphisms in wild populations. In 30 wild individuals, the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average PIC value was 0.8. These microsatellite markers should prove to be a useful addition to the microsatellite markers that are now available for this species.

  17. Apomixis in different ploidy levels of cassava.

    PubMed

    Nassar, Nagib M A; Chaib, Adalgisa; Elsayed, Ahmed Y

    2011-11-01

    Two polyploid hybrids between cassava (Manihot esculenta) cultivar 307-2 and its wild relatives M. glaziovii and M. anomala, were studied to examine the relationship between ploidy level and the production of seeds without fertilization. A clearing method was applied to assess ovule sizes as an indication of multiembryony. The diploid cultivar 307-2 had regular 18 bivalents at meiotic metaphase 1 while the polyploid types showed chromosome configurations varying from 3 to 4 quadrivalents and 28 to 30 bivalents. A total of 14% of studied ovules of the polyploid hybrid involving M. glaziovii were multiebryonic, while the percentage of multiembryony was as low as 2% in the polyploid hybrid M. anomala×M. esculenta. Diploid hybrid types did not show any multi embryony. Adventitious embryos were found and documented for the first time in polyploid hybrids M. esculenta×M. glaziovii. The association of multiple embryo formation with ovary size and pollination showed that apomictic embryos form independently from fertilization. Simple iodized carmine stain for measuring pollen viability proved as efficient as the sophisticated Alexander method.

  18. Survey and Analysis of Microsatellites in the Silkworm, Bombyx mori

    PubMed Central

    Prasad, M. Dharma; Muthulakshmi, M.; Madhu, M.; Archak, Sunil; Mita, K.; Nagaraju, J.

    2005-01-01

    We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of ≥15 bases of mononucleotide repeats and ≥5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2–14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama. PMID:15371363

  19. A polymorphic indel containing the RS3 microsatellite in the 5' flanking region of the vasopressin V1a receptor gene is associated with chimpanzee (Pan troglodytes) personality.

    PubMed

    Hopkins, W D; Donaldson, Z R; Young, L J

    2012-07-01

    Vasopressin is a neuropeptide that has been strongly implicated in the development and evolution of complex social relations and cognition in mammals. Recent studies in voles have shown that polymorphic variation in the promoter region of the arginine vasopressin V1a receptor gene (avpr1a) is associated with different dimensions of sociality. In humans, variation in a repetitive sequence element in the 5' flanking region of the AVPR1A, known as RS3, have also been associated with variation in AVPR1a gene expression, brain activity and social behavior. Here, we examined the association of polymorphic variation in this same 5' flanking region of the AVPR1A on subjective ratings of personality in a sample of 83 chimpanzees (Pan troglodytes). Initial analyses indicated that 34 females and 19 males were homozygous for the short allele, which lacks RS3 (DupB(-/-)), while 18 females and 12 males were heterozygous and thus had one copy of the long allele containing RS3 (DupB(+/-)), yielding overall allelic frequencies of 0.82 for the DupB(-) allele and 0.18 for the DupB(+) allele. DupB(+/+) chimpanzees were excluded from the analysis because of the limited number of individuals. Results indicated no significant sex difference in personality between chimpanzees homozygous for the deletion of the RS3-containing DupB region (DupB(-/-)); however, among chimpanzees carrying one allele with the DupB present (DupB(+/-)), males had significantly higher dominance and lower conscientiousness scores than females. These findings are the first evidence showing that the AVPR1A gene plays a role in different aspects of personality in male and female chimpanzees.

  20. Evaluation of ploidy level and endoreduplication in carnation (Dianthus spp.).

    PubMed

    Agulló-Antón, María Ángeles; Olmos, Enrique; Pérez-Pérez, José Manuel; Acosta, Manuel

    2013-03-01

    Carnation (Dianthus caryophyllus L.) is one of the fifth most important ornamental species worldwide. Many desirable plant characteristics, such as big size, adaptation under stress, and intra or interspecific hybridization capability, are dependent on plant ploidy level. We optimized a quick flow cytometry method for DNA content determination in wild and cultivated carnation samples that allowed a systematic evaluation of ploidy levels in Dianthus species. The DNA content of different carnation cultivars and wild Dianthus species was determined using internal reference standards. The precise characterization of ploidy, endoreduplication and C-value of D. caryophyllus 'Master' makes it a suitable standard cultivar for ploidy level determination in other carnation cultivars. Mixoploidy was rigorously characterized in different regions of several organs from D. caryophyllus 'Master', which combined with a detailed morphological description suggested some distinctive developmental traits of this species. Both the number of endoreduplication cycles and the proportion of endopolyploid cells were highly variable in the petals among the cultivars studied, differently to the values found in leaves. Our results suggest a positive correlation between ploidy, cell size and petal size in cultivated carnation, which should be considered in breeding programs aimed to obtain new varieties with large flowers.

  1. Effect of ploidy increase on transgene expression: example from Citrus diploid cybrid and allotetraploid somatic hybrid expressing the EGFP gene.

    PubMed

    Xu, Shi-Xiao; Cai, Xiao-Dong; Tan, Bin; Li, Ding-Li; Guo, Wen-Wu

    2011-07-01

    Polyploidization is an important speciation mechanism for all eukaryotes, and it has profound impacts on biodiversity dynamics and ecosystem functioning. Green fluorescent protein (GFP) has been used as an effective marker to visually screen somatic hybrids at an early stage in protoplast fusion. We have previously reported that the intensity of GFP fluorescence of regenerated embryoids was also an early indicator of ploidy level. However, little is known concerning the effects of ploidy increase on the GFP expression in citrus somatic hybrids at the plant level. Herein, allotetraploid and diploid cybrid plants with enhanced GFP (EGFP) expression were regenerated from the fusion of embryogenic callus protoplasts from 'Murcott' tangor (Citrus reticulata Blanco × Citrus sinensis (L.) Osbeck) and mesophyll protoplasts from transgenic 'Valencia' orange (C. sinensis (L.) Osbeck) expressing the EGFP gene, via electrofusion. Subsequent simple sequence repeat (SSR), chloroplast simple sequence repeat and cleaved amplified polymorphic sequence analysis revealed that the two regenerated tetraploid plants were true allotetraploid somatic hybrids possessing nuclear genomic DNA of both parents and cytoplasmic DNA from the callus parent, while the five regenerated diploid plants were cybrids containing nuclear DNA of the leaf parent and with complex segregation of cytoplasmic DNA. Furthermore, EGFP expression was compared in cells and protoplasts from mature leaves of these diploid cybrids and allotetraploid somatic hybrids. Results showed that the intensity of GFP fluorescence per cell or protoplast in diploid was generally brighter than in allotetraploid. Moreover, same hybridization signal was detected on allotetraploid and diploid plants by Southern blot analysis. By real-time RT-PCR and Western blot analysis, GFP expression level of the diploid cybrid was revealed significantly higher than that of the allotetraploid somatic hybrid. These results suggest that ploidy

  2. How to halve ploidy: lessons from budding yeast meiosis.

    PubMed

    Kerr, Gary William; Sarkar, Sourav; Arumugam, Prakash

    2012-09-01

    Maintenance of ploidy in sexually reproducing organisms requires a specialized form of cell division called meiosis that generates genetically diverse haploid gametes from diploid germ cells. Meiotic cells halve their ploidy by undergoing two rounds of nuclear division (meiosis I and II) after a single round of DNA replication. Research in Saccharomyces cerevisiae (budding yeast) has shown that four major deviations from the mitotic cell cycle during meiosis are essential for halving ploidy. The deviations are (1) formation of a link between homologous chromosomes by crossover, (2) monopolar attachment of sister kinetochores during meiosis I, (3) protection of centromeric cohesion during meiosis I, and (4) suppression of DNA replication following exit from meiosis I. In this review we present the current understanding of the above four processes in budding yeast and examine the possible conservation of molecular mechanisms from yeast to humans.

  3. FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

    PubMed Central

    Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

    2016-01-01

    Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID

  4. Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

    PubMed Central

    Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff; Elshire, Rob; Cherney, Jerome H.; Casler, Michael D.; Buckler, Edward S.; Costich, Denise E.

    2013-01-01

    Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of

  5. Development of microsatellite markers for Hancornia speciosa Gomes (Apocynaceae).

    PubMed

    Rodrigues, A J L; Yamaguishi, A T; Chaves, L J; Coelho, A S G; Lima, J S; Telles, M P C

    2015-07-03

    Herein, we describe 34 microsatellite loci developed using an enrichment genomic library for the tree species Hancornia speciosa Gomes (Apocynaceae). Thirty-five individuals were genotyped using 34 primers to analyze the polymorphisms at each locus. The number of alleles per locus ranged from 4 to 20. The average number of alleles was 8.11, and the expected heterozygosity ranged from 0.62 to 0.94. These microsatellite primers will be useful in population genetics studies for this species.

  6. Multiplexed microsatellite recovery using massively parallel sequencing.

    PubMed

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  7. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  8. Microsatellite markers for Russian olive (Elaeagnus angustifolia; Elaeagnaceae)1

    PubMed Central

    Gaskin, John F.; Hufbauer, Ruth A.; Bogdanowicz, Steven M.

    2013-01-01

    • Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. • Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. • Conclusions: These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion. PMID:25202584

  9. Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

    PubMed Central

    López-Roberts, M. Cristina; Barbosa, Ariane R.; Paganucci de Queiroz, Luciano; van den Berg, Cássio

    2016-01-01

    Premise of the study: Senna spectabilis var. excelsa (Fabaceae) is a South and Central American tree of great ecological importance and one of the most common species in several sites of seasonally dry forests. Our goal was to develop microsatellite markers to assess the genetic diversity and structure of this species. Methods and Results: We designed and assessed 53 loci obtained from a microsatellite-enriched library and an intersimple sequence repeat library. Fourteen loci were polymorphic, and they presented a total of 39 alleles in a sample of 61 individuals from six populations. The mean values of observed and expected heterozygosities were 0.355 and 0.479, respectively. Polymorphism information content was 0.390 and the Shannon index was 0.778. Conclusions: Polymorphism information content and Shannon index indicate that at least nine of the 14 microsatellite loci developed are moderate to highly informative, and potentially useful for population genetic studies in this species. PMID:26819856

  10. Ecogeography of ploidy variation in cultivated potato (Solanum sect. Petota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3 to 17. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, containing diploid (2 n = 2 x = 24), triploid (2 n = 3 x = 36), tetr...

  11. Ecogeography of Ploidy Variation in Cultivated Potato (Solanum Sect. Petota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3-18. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, with diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = ...

  12. A microsatellite genetic linkage map of black rockfish ( Sebastes schlegeli)

    NASA Astrophysics Data System (ADS)

    Chu, Guannan; Jiang, Liming; He, Yan; Yu, Haiyang; Wang, Zhigang; Jiang, Haibin; Zhang, Quanqi

    2014-12-01

    Ovoviviparous black rockfish ( Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 cM and average inter-marker space of 13.3 cM. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 cM and average inter-marker distance of 12.4 cM. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

  13. Use of eyeballs for establishing ploidy of Asian carp

    USGS Publications Warehouse

    Jenkins, J.A.; Thomas, R.G.

    2007-01-01

    Grass carp Ctenopharyngodon idella, silver carp Hypophthalmichthys molitrix, and bighead carp H. nobilis are now established and relatively common in the Mississippi and Atchafalaya rivers. Commercial fishers of Louisiana's large rivers report recurrent catches of grass carp, and the frequency of bighead carp and silver carp catch is increasing. Twelve black carp Mylopharyngodon piceus were recently captured from the Mississippi and Atchafalaya River system, and 10 were analyzed for ploidy. By using the methods described herein, all 10 fish were determined to be diploid. Such correct identifications of ploidy of feral Asian carp species, as well as other species, would provide science-based information constructive for meeting reporting requirements, tracking fish movements, and forecasting expansion of species distribution. To investigate the postmortem period for sample collection and to lessen demands on field operations for obtaining samples, a laboratory study was performed to determine the length of time for which eyeballs from postmortem black carp could be used for ploidy determinations. Acquiring eyes rather than blood is simpler and quicker and requires no special supplies. An internal DNA reference standard with a documented genome size, including erythrocytes from diploid black carp or Nile tilapia Oreochromis niloticus, was analyzed simultaneously with cells from seven known triploid black carp to assess ploidy through 12 d after extraction. Ploidy determinations were reliable through 8 d postmortem. The field process entails excision of an eyeball, storage in a physiological buffer, and shipment within 8 d at refrigeration temperatures (4??C) to the laboratory for analysis by flow cytometry. ?? Copyright by the American Fisheries Society 2007.

  14. Isolation and characterization of microsatellite loci in Quercus fabri (Fagaceae).

    PubMed

    Xiao, Z Z; Chen, W W; Bao, W; Wang, R; Li, Y Y

    2016-06-21

    Quercus fabri is a pioneer species of secondary succession in evergreen broadleaved forests in China. In this study, we isolated and developed 12 polymorphic and 2 monomorphic microsatellite loci for Q. fabri using the biotin-streptavidin capture method. We characterized 12 polymorphic loci in 52 individuals from two populations. The number of alleles per locus ranged from 3 to 23. The observed and expected heterozygosities per locus were 0.033-0.773 and 0.138-0.924, respectively. These microsatellite loci will facilitate the studies on genetic variation, mating system, and gene flow of Q. fabri.

  15. Disturbances in the ploidy level in the gynogenetic sterlet Acipenser ruthenus.

    PubMed

    Fopp-Bayat, D; Ocalewicz, K; Kucinski, M; Jankun, M; Laczynska, B

    2017-02-06

    Artificial mitotic gynogenesis, a chromosome set manipulation, is applied to provide the homozygous progeny with only maternal inheritance. Here, gynogenetic development was induced in the sterlet Acipenser ruthenus L. (Acipenseridae) by activation of the eggs originating from albino females with the UV-irradiated spermatozoa from wild-coloured males, followed by the heat shock applied to suppress the first mitotic division in the haploid zygotes. All experimentally obtained gynogenetic offspring possessed recessive albino coloration. Moreover, the genetic verification, based on three microsatellite DNA markers, confirmed the only maternal inheritance in the albino progeny. Cytogenetic screening enabled identification of the aneuploids, haploids, diploids, triploids, tetraploids and mosaic individuals among the gynogenetic larvae that hatched from the eggs subjected to the heat shock. Furthermore, 40% of the larvae from the haploid variants of the research that were not exposed to the temperature shock showed the diploid chromosome number. A variation of the ploidy level observed in the gynogenetic sterlets may be the consequence of the spontaneous polyploidisation that occurred in the haploid zygotes. Moreover, observation during embryogenesis showed varied stages of eggs development and the asynchronous cell cleavages that may have resulted in the chromosomal disturbances observed in the gynogenetic sterlets here.

  16. Diploid Musa acuminata genetic diversity assayed with sequence-tagged microsatellite sites.

    PubMed

    Grapin, A; Noyer, J L; Carreel, F; Dambier, D; Baurens, F C; Lanaud, C; Lagoda, P J

    1998-06-01

    The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.

  17. Isolation and characterisation of the first microsatellite markers for Cyperus rotundus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cyperus rotundus L. (purple nutsedge), is a weed that affects crops as cotton, soybean and vegetables, mainly in the South of the United States. We have developed 191 microsatellite markers, 39% of them being polymorphic when tested on 13 accessions of this weed. The microsatellites evidenced gene...

  18. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE EUROPEAN GREEN CRAB (CARCINUS MAENAS)

    EPA Science Inventory

    Carcinus maenas (Decapoda: Portunidae) has proven a highly successful invasive marine species whose potential economic and ecological impacts are of great concern worldwide. Here, we characterize fourteen polymorphic microsatellite loci in C. maenas and its sister species C. Ae...

  19. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE WIDELY INTRODUCED ESTUARINE ANEMONE NEMATOSTELLA VECTENSIS

    EPA Science Inventory

    We characterized ten polymorphic microsatellite loci from Nematostella vectensis, a burrowing anemone recently introduced to estuaries along the Pacific coast of North America and the southeast coast of England. Preliminary results indicate high variability and significant depar...

  20. Sequence-tagged microsatellite sites as markers in chicken reference and resource populations.

    PubMed

    Khatib, H; Genislav, E; Crittenden, L B; Bumstead, N; Soller, M

    1993-10-01

    Two chicken genomic libraries were screened for the presence of poly(TG/AC) microsatellite tracts. The number of positive clones was low, confirming the low frequency of such microsatellites in the chicken genome relative to mammalian genomes. Polymorphism of 29 microsatellite tracts, comprising 11 from the library screening and 18 obtained from GenBank, was examined in the East Lansing and Compton reference families, in a resource population formed by a cross between a single White Rock broiler and inbred Leghorn females, and in a panel of birds from five layer stocks. Twenty microsatellites, primarily of the poly(TG/AC) type, were polymorphic in at least one of the populations. Thirteen of the microsatellites were polymorphic in the East Lansing reference family and 13 were also polymorphic in the resource population, confirming that the genetic distance between White Rock and White Leghorn is about as great as between Jungle fowl and White Leghorn. Only six microsatellites were polymorphic in the Compton reference family, formed by a cross between two White Leghorn strains. Twelve of the microsatellites were mapped in the East Lansing and/or Compton reference families. These were well dispersed among the various linkage groups and did not show any indications of terminal clustering.

  1. The Polyploid Series of the Achillea millefolium Aggregate in the Iberian Peninsula Investigated Using Microsatellites

    PubMed Central

    López-Vinyallonga, Sara; Soriano, Ignasi; Susanna, Alfonso; Montserra, Josep Maria; Roquet, Cristina; Garcia-Jacas, Núria

    2015-01-01

    The Achillea millefolium aggregate is one of the most diverse polyploid complexes of the Northern hemisphere and has its western Eurasian boundary in the Iberian Peninsula. Four ploidy levels have been detected in A. millefolium, three of which have already been found in Iberia (diploid, hexaploid and octoploid), and a fourth (tetraploid) reported during the preparation of this paper. We collected a sample from 26 Iberian populations comprising all ploidy levels, and we used microsatellite markers analyzed as dominant in view of the high ploidy levels. Our goals were to quantify the genetic diversity of A. millefolium in the Iberian Peninsula, to elucidate its genetic structure, to investigate the differences in ploidy levels, and to analyse the dispersal of the species. The lack of spatial genetic structure recovered is linked to both high levels of gene flow between populations and to the fact that most genetic variability occurs within populations. This in turn suggests the existence of a huge panmictic yarrow population in the Iberian Peninsula. This is consistent with the assumption that recent colonization and rapid expansion occurred throughout this area. Likewise, the low levels of genetic variability recovered suggest that bottlenecks and/or founder events may have been involved in this process, and clonal reproduction may have played an important role in maintaining this genetic impoverishment. Indeed, the ecological and phenologic uniformity present in the A. millefolium agg. in Iberia compared to Eurasia and North America may be responsible for the low number of representatives of this complex of species present in the Iberian Peninsula. The low levels of genetic differentiation between ploidy levels recovered in our work suggest the absence of barriers between them. PMID:26091537

  2. Atypical ploidy cycles, Spo11, and the evolution of meiosis.

    PubMed

    Bloomfield, Gareth

    2016-06-01

    The Spo11 protein induces DNA double strand breaks before the first division of meiosis, enabling the formation of the chiasmata that physically link homologous chromosomes as they align. Spo11 is an ancient and well conserved protein, related in sequence and structure to a DNA topoisomerase subunit found in Archaea as well as a subset of eukaryotes. However the origins of its meiotic function are unclear. This review examines some apparent exceptions to the rule that Spo11 activity is specific to, and required for meiosis. Spo11 appears to function in the context of unusual forms of ploidy reduction in some protists and fungi. One lineage of amoebae, the dictyostelids, is thought to undergo meiosis during its sexual cycle despite having lost Spo11 entirely. Further experimental characterisation of these and other non-canonical ploidy cycling mechanisms may cast light of the evolution of meiosis.

  3. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Giraldo, M C; Buendía, H F; Tovar, E; Duque, M C; Beebe, S E

    2006-06-01

    A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity

  4. Host-parasite interactions and the evolution of ploidy.

    PubMed

    Nuismer, Scott L; Otto, Sarah P

    2004-07-27

    Although the majority of animals and plants, including humans, are dominated by the diploid phase of their life cycle, extensive diversity in ploidy level exists among eukaryotes, with some groups being primarily haploid whereas others alternate between haploid and diploid phases. Previous theory has illuminated conditions that favor the evolution of increased or decreased ploidy but has shed little light on which species should be primarily haploid and which primarily diploid. Here, we report a discovery that emerged from host-parasite models in which ploidy levels were allowed to evolve: selection is more likely to favor diploidy in host species and haploidy in parasite species. Essentially, when parasites must evade a host's immune system or defense response, selection favors parasitic individuals that express a narrow array of antigens and elicitors, thus favoring haploid parasites over diploid parasites. Conversely, when hosts must recognize a parasite before mounting a defensive response, selection favors hosts with a broader arsenal of recognition molecules, thus favoring diploid hosts over haploid hosts. These results are consistent with the predominance of haploidy among parasitic protists.

  5. A microsatellite linkage map of striped bass (Morone saxatilis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Striped bass (Morone saxatilis) is of great importance for fisheries and aquaculture in the US. To construct a linkage map of striped bass, 480 microsatellite markers were screened for polymorphism among three parents of two half-sib mapping families that shared a common dam. A total of 289 markers ...

  6. Microsatellite loci for the invasive colonial hydrozoan Cordylophora caspia

    EPA Science Inventory

    Cordylophora caspia, a colonial hydrozoan native to the Ponto-Caspian region, has become a common invader of both fresh and brackish water ecosystems of North America and Europe. Here we describe 11 polymorphic microsatellite loci for this species. Preliminary analyses indicate ...

  7. Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity

    PubMed Central

    2011-01-01

    Because of the high mutation rate of microsatellites, polymorphism at microsatellite loci might be predicted to reflect the effective population size over a time span of about 10,000 years and thus to be associated with biogeographic factors impacting species on that time frame. This prediction was tested by comparing heterozygosity at microsatellite loci from 294 bird species, including 58 species endemic to oceanic islands. Controlling statistically for phylogenetic effects, mean heterozygosity was significantly reduced in oceanic island endemics compared to other species. There was also an effect of current endangerment, statistically independent of the effect of island endemicity. These results support the hypothesis that long-term effective population size can be an important causative factor behind differences among species with respect to microsatellite heterozygosity. PMID:21104002

  8. Development and characterization of microsatellite primers for Chamaecyparis obtusa (Cupressaceae)1

    PubMed Central

    Kim, Young Mi; Shin, Yu Seung; Jeong, Ji Hee

    2016-01-01

    Premise of the study: Although several microsatellite markers of Chamaecyparis obtusa (Cupressaceae) have been reported in previous studies, we newly developed and evaluated polymorphic microsatellite markers of C. obtusa, an economically important species in Korea as a major forestation tree species, for further genetic studies. Methods and Results: Microsatellite-enrichment libraries were constructed according to the selective hybridization method. From this output, we obtained 10 polymorphic and five monomorphic microsatellite markers for C. obtusa. Five of these developed markers were successfully amplified for C. pisifera, a related species. Conclusions: These microsatellite markers can be valuable tools for further genetic studies of C. obtusa, and gathered genetic information may be useful for breeding program management. PMID:27213124

  9. Development and characterization of microsatellite primers in the endangered Mediterranean shrub Ziziphus lotus (Rhamnaceae)1

    PubMed Central

    González-Robles, Ana; Manzaneda, Antonio J.; Bastida, Jesús M.; Harvey, Nick; Jaime, Rafael; Salido, Teresa; Martínez, Luisa M.; Fernández-Ocaña, Ana; Alcántara, Julio M.; Rey, Pedro J.

    2016-01-01

    Premise of the study: Microsatellite primers were developed to characterize and evaluate patterns of genetic diversity and structure in the endangered Mediterranean shrub Ziziphus lotus (Rhamnaceae). Methods and Results: Twenty microsatellite primers were developed for Z. lotus, of which 14 were polymorphic. We evaluated microsatellite polymorphism in 97 specimens from 18 Spanish and seven Moroccan populations. Between two and eight alleles were found per locus, and the average number of alleles was 5.54. Observed heterozygosity and expected heterozygosity ranged from 0.08 to 0.90 and from 0.08 to 0.82, respectively. Nine of these primers also amplified microsatellite loci in Z. jujuba. Conclusions: The microsatellite markers described here will be useful in studies on genetic variation, population genetic structure, and gene flow in the fragmented habitat of this species. These markers are a valuable resource for designing appropriate conservation measures for the species in the Mediterranean range. PMID:28101436

  10. Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species1

    PubMed Central

    Prebble, Jessica M.; Tate, Jennifer A.; Meudt, Heidi M.; Symonds, V. Vaughan

    2015-01-01

    Premise of the study: Microsatellite loci were developed as polymorphic markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) for use in species delimitation and population and conservation genetic studies. Methods and Results: Illumina MiSeq sequencing was performed on genomic DNA from seedlings of M. drucei. From trimmed paired-end sequences >400 bp, 484 microsatellite loci were identified. Twelve of 48 microsatellite loci tested were found to be polymorphic and consistently scorable when screened on 53 individuals from four populations representing the geographic range of M. drucei. They also amplify in all other species in the M. pygmaea species group, i.e., M. antarctica, M. brevis, M. glauca, and M. pygmaea, as well as 18 other Myosotis species. Conclusions: These 12 polymorphic microsatellite markers establish an important resource for research and conservation of the M. pygmaea species group and potentially other Southern Hemisphere Myosotis. PMID:26082880

  11. Microsatellite instability confounds engraftment analysis of hematopoietic stem-cell transplantation.

    PubMed

    Tseng, Li-Hui; Tang, Jih-Luh; Haley, Lisa; Beierl, Katie; Gocke, Christopher D; Eshleman, James R; Lin, Ming-Tseh

    2014-07-01

    Polymorphic short tandem-repeat, or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem-cell transplantation. In molecular diagnostic laboratories, it is recommended to calculate mixed chimerism for at least 2 informative loci and to avoid microsatellite loci on chromosomes with copy number changes. In this report, we show that microsatellite instability observed in 2 patients with acute leukemia may confound chimerism analysis. Interpretation errors may occur even if 2 to 3 loci are analyzed because of length variation in multiple microsatellite loci. Although microsatellite loci with length variation should not be selected for chimerism analysis, the presence of microsatellite instability, like copy number alteration because of aberrant chromosomes, provides evidence of recurrent or residual cancer cells after hematopoietic stem-cell transplantation.

  12. Twenty microsatellite markers for the endangered Vatica mangachapoi (Dipterocarpaceae)1

    PubMed Central

    Guo, Jun-Jie; Shang, Shuai-Bin; Wang, Chun-Sheng; Zhao, Zhi-Gang; Zeng, Jie

    2017-01-01

    Premise of the study: Microsatellite markers were developed for Vatica mangachapoi (Dipterocarpaceae), an endangered species indigenous to Southeast Asia and southern China. Methods and Results: Twenty microsatellite markers, including 12 polymorphic markers, were identified from V. mangachapoi using high-throughput sequencing. Polymorphism at each marker was evaluated using 87 individuals from three natural populations. The number of alleles per polymorphic locus ranged from six to 15, and the observed and expected heterozygosity varied from 0.000 to 0.926 and from 0.177 to 0.864, respectively. These markers were transferred successfully to the endangered species V. guangxiensis. Conclusions: These markers may be used to investigate the genetic diversity and gene flow of V. mangachapoi and V. guangxiensis. PMID:28224060

  13. New microsatellite markers for bananas (Musa spp).

    PubMed

    Amorim, E P; Silva, P H; Ferreira, C F; Amorim, V B O; Santos, V J; Vilarinhos, A D; Santos, C M R; Souza Júnior, M T; Miller, R N G

    2012-04-27

    Thirty-four microsatellite markers (SSRs) were identified in EST and BAC clones from Musa acuminata burmannicoides var. Calcutta 4 and validated in 22 Musa genotypes from the Banana Germplasm Bank of Embrapa-CNPMF, which includes wild and improved diploids. The number of alleles per locus ranged from 2 to 14. The markers were considered highly informative based on their polymorphism information content values; more than 50% were above 0.5. These SSRs will be useful for banana breeding programs, for studies of genetic diversity, germplasm characterization and selection, development of saturated genetic linkage maps, and marker assisted selection.

  14. Variogram Analysis of the Spatial Genetic Structure of Continuous Populations Using Multilocus Microsatellite Data

    PubMed Central

    Wagner, Helene H.; Holderegger, Rolf; Werth, Silke; Gugerli, Felix; Hoebee, Susan E.; Scheidegger, Christoph

    2005-01-01

    A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation. PMID:15654102

  15. DNA ploidy and proliferation heterogeneity in human prostate cancers

    SciTech Connect

    Shankey, T.V.; Graham, S. |; Dougherty, S.

    1995-09-01

    DNA ploidy determinations have been shown to have clinical application in predicting disease progression, survival, or response to anti-androgen therapies in prostate carcinomas. Since intra-tumor heterogeneity may have a profound effect on DNA measurements, we determined the frequency of DNA ploidy and proliferation (here S-phase fraction) heterogeneity in early prostatic carcinomas, and estimated the potential impact of heterogeneity on predicting disease course, survival, or response to therapy. Using image and flow cytometric analysis of archival, paraffin-embedded prostate tumors, we measured DNA ploidy in individual foci of prostatic carcinoma in stage T1a, T1b and T1c disease. Our results indicate that DNA aneuploid foci of prostate carcinoma are infrequently seen in stage T1a disease (13% of the individuals studied), and that the presence of both DNA diploid and aneuploid foci in the same sample is seen in less than 10% of these individuals. Stage T1b and T1c tumors containing only DNA diploid nuclei are seen, though these are likely most common in low volume, low Gleason grade tumors. By using flow cytometry to compare these results with those using image analysis of the same tumor foci, we demonstrated that the majority (>75%) of these aneuploid tumors are DNA tetraploid. Our data on prostate tumor S-phase fractions indicate that DNA diploid tumors generally have a lower S-phase than DNA aneuploid foci (including comparisons of DNA diploid and aneuploid foci in the same prostate tumor). These results support the model that early prostate tumors are DNA diploid and have a low S-phase, and that these tumors likely evolve to DNA tetraploid tumors with a similar low S-phase fraction. 25 refs., 4 figs., 4 tabs.

  16. Characterization of 11 new microsatellite loci in taro (Colocasia esculenta).

    PubMed

    Hu, Kan; Huang, Xing Fang; Ke, Wei Dong; Ding, Yi

    2009-03-01

    Eleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty-eight primer pairs were designed from a microsatellite-enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.

  17. Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

    USGS Publications Warehouse

    John, J. St; Kysela, R.F.; Oyler-McCance, S.J.

    2007-01-01

    Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species' range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover. ?? 2007 Blackwell Publishing Ltd.

  18. Reproductive isolation and hybridization in sympatric populations of three Dactylorhiza species (Orchidaceae) with different ploidy levels

    PubMed Central

    De hert, Koen; Jacquemyn, Hans; Van Glabeke, Sabine; Roldán-Ruiz, Isabel; Vandepitte, Katrien; Leus, Leen; Honnay, Olivier

    2012-01-01

    Background and Aims The potential for gene exchange between species with different ploidy levels has long been recognized, but only a few studies have tested this hypothesis in situ and most of them focused on not more than two co-occurring species. In this study, we examined hybridization patterns in two sites containing three species of the genus Dactylorhiza (diploid D. incarnata and D. fuchsii and their allotetraploid derivative D. praetermissa). Methods To compare the strength of reproductive barriers between diploid species, and between diploid and tetraploid species, crossing experiments were combined with morphometric and molecular analyses using amplified fragment length polymorphism markers, whereas flow cytometric analyses were used to verify the hybrid origin of putative hybrids. Key Results In both sites, extensive hybridization was observed, indicating that gene flow between species is possible within the investigated populations. Bayesian assignment analyses indicated that the majority of hybrids were F1 hybrids, but in some cases triple hybrids (hybrids with three species as parents) were observed, suggesting secondary gene flow. Crossing experiments showed that only crosses between pure species yielded a high percentage of viable seeds. When hybrids were involved as either pollen-receptor or pollen-donor, almost no viable seeds were formed, indicating strong post-zygotic reproductive isolation and high sterility. Conclusions Strong post-mating reproductive barriers prevent local breakdown of species boundaries in Dactylorhiza despite frequent hybridization between parental species. However, the presence of triple hybrids indicates that in some cases hybridization may extend the F1 generation. PMID:22186278

  19. Relationship between DNA ploidy level and tumor sociology behavior in 12 nervous cell lines

    SciTech Connect

    Kiss, R.; Camby, I.; Salmon, I.

    1995-06-01

    Cell population sociology was studied in two medulloblastomas and 10 astrocytic human tumor cell lines by means of the characterization of the structure of neoplastic cell colonies growing on histological slides. This was carried out via digital cell image analysis of Feulgen-stained nuclei, to which the Delaunay triangulation and Voronoi paving mathematical techniques were applied. Such assessments were compared to the DNA ploidy level (assessed by means of DNA histogram typing). The results show that the cell colony architecture characteristics differed markedly according to whether the cell lines were euploid (diploid or tetraploid) or aneuploid (hyperdiploid, triploid, hypertriploid, or polymorphic). In fact, the cell colonies from the euploid cell nuclei populations were larger and more dense than those from the aneuploid ones. Furthermore, for an identical period of culture, the cell lines from high-grade malignant astrocytic tumors (glioblastomas) exhibited cell colonies that were larger and more dense than those in cell lines from low-grade astrocytic tumors (astrocytomas). In each of these two groups, the diploid cell nuclei populations exhibited cell colonies larger and more dense than the nondiploid colonies. The present methodology is now being applied in vivo to histological sections of surgically removed human brain tumors in order to distinguish between high-risk clinical subgroups and medium-risk subgroups in clearly circumscribed histopathological groups. 38 refs., 5 figs., 2 tabs.

  20. Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

    PubMed Central

    Zhou, He; Ma, Tian-Yu; Zhang, Rui; Xu, Qi-Zheng; Shen, Fu; Qin, Yan-Jie; Xu, Wen; Wang, Yuan; Li, Ya-Juan

    2016-01-01

    In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively. PMID:27556458

  1. Development and characterization of 23 microsatellite loci for Rhododendron ovatum (Ericaceae)1

    PubMed Central

    Liu, De-Chen; Zhang, Yang; Wang, Si-Si; Liao, Meng-Yu; Fan, Xin-Yu; Li, Yuan-Yuan; Wang, Rong

    2017-01-01

    Premise of the study: To estimate the genetic variation of Rhododendron ovatum (Ericaceae), a monoecious evergreen shrub, 23 microsatellite markers were identified from its nuclear genome. Methods and Results: We developed 16 polymorphic and seven monomorphic microsatellite primers using the biotin-streptavidin capture method. The 16 polymorphic loci were investigated further using 89 individuals sampled from three populations in China. The number of alleles per locus ranged from four to 30, indicating a high level of polymorphism. The observed heterozygosity varied from 0.1034 to 0.9333, while the expected heterozygosity ranged from 0.1016 to 0.9542. Of these polymorphic primers, 12 were found to be functional in R. simsii, a congeneric species of R. ovatum. Conclusions: Moderate to high levels of genetic variation were found in these microsatellite loci, indicating that they can be applied in future studies of Rhododendron genetic structure, contributing to forest management and conservation. PMID:28090409

  2. Characterization and development of chloroplast microsatellite markers for Gossypium hirsutum, and cross-species amplification in other Gossypium species.

    PubMed

    Cai, X Y; Liu, F; Zhou, Z L; Wang, X X; Wang, C Y; Wang, Y H; Wang, K B

    2015-10-05

    Cotton is an important economic crop worldwide; its fiber, commonly known as cotton lint, is the main natural source for the textile industry. Sixty chloroplast microsatellites were identified and characterized from the complete sequence of the Gossypium hirsutum chloroplast genome using a bioinformatic approach. Twenty chloroplast microsatellite loci were polymorphic in the 66 Gossypium germplasm accessions. A total of 85 alleles were detected, with allele numbers varying from 2-7 per locus. Polymorphism information content varied from 0.02-0.66, with a mean of 0.48. Additionally, transferability of the 20 polymorphic chloroplast microsatellite primers was evaluated in other 31 Gossypium species. Sixteen markers were successfully amplified across all species tested, while the remaining 4 markers cross-amplified in most species tested. These polymorphic chloroplast microsatellite markers may be useful tool for studies of individual identification, genetic diversity, evolution, conservation genetics, and molecular breeding in Gossypium.

  3. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    PubMed

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  4. Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis).

    PubMed

    Doyle, Jacqueline M; Siegmund, Gregor; Ruhl, Joseph D; Eo, Soo Hyung; Hale, Matthew C; Marra, Nicholas J; Waser, Peter M; Dewoody, J Andrew

    2013-07-01

    Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes.

  5. Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

    PubMed Central

    Sawaya, Sterling; Bagshaw, Andrew; Buschiazzo, Emmanuel; Kumar, Pankaj; Chowdhury, Shantanu; Black, Michael A.; Gemmell, Neil

    2013-01-01

    Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context. PMID:23405090

  6. Characterization of vasa in the gonads of different ploidy fish.

    PubMed

    Yu, Fan; Zhong, Huan; Liu, Gang; Liu, Shaojun; Zhang, Zhuohui; Zhou, Yi; Tao, Min; Liu, Yun

    2015-12-15

    Vasa is an essential gene for germ cell development belonging to the DEAD-box family. In this study, we comparatively analyzed the expression characteristics of vasa in diploids, triploids, and tetraploids. The sequences showed high similarity among these fish and other vertebrates, with characteristic domains. Tissue expression analysis revealed that vasa was expressed exclusively in the gonad of different ploidy fishes. During embryogenesis, vasa expression was lower in diploid than in triploid and tetraploid fish, caused by doubling of the genome of tetraploids and abnormal gonads in the triploid fish. In adults, vasa mRNA levels were significantly lower in the testes of sterile triploid fish compared with fertile diploids and tetraploids. In the ovaries, triploid fish showed consistently high expression from the non-breeding season to the breeding season. Immunohistochemistry and western blotting results also supported the abnormal expression of vasa in triploid gonads. This study demonstrates, for the first time, that fish of different ploidy exhibit different expression patterns of vasa that contribute to the differentiation of gonadal development.

  7. PERMANENT GENETIC RESOURCES: Isolation and characterization of nine microsatellite loci from the chub mackerel, Scomber japonicus (Perciformes, Scombridae).

    PubMed

    Yagishita, N; Kobayashi, T

    2008-03-01

    The stock abundance of the chub mackerel Scomber japonicus - a very important species for fisheries, particularly in Japan - in the Pacific Ocean off Japan has remained at a low level. For studying the population genetics of the chub mackerel, we isolated nine polymorphic microsatellite loci (12-31 alleles/locus; expected heterozygosity, 0.762-0.983) from this species. Cross-species amplification indicated that eight of the nine microsatellite loci in the blue mackerel S. australasicus were polymorphic and functional.

  8. Biogeographic variation in genetic variability, apomixis expression and ploidy of St. John's wort (Hypericum perforatum) across its native and introduced range

    PubMed Central

    Molins, Marta Puente; Corral, José M.; Aliyu, Olawale Mashood; Koch, Marcus A.; Betzin, Anja; Maron, John L.; Sharbel, Timothy F.

    2014-01-01

    Background and Aims St. John's wort (Hypericum perforatum) is becoming an important model plant system for investigations into ecology, reproductive biology and pharmacology. This study investigates biogeographic variation for population genetic structure and reproduction in its ancestral (European) and introduced (North America) ranges. Methods Over 2000 individuals from 43 localities were analysed for ploidy, microsatellite variation (19 loci) and reproduction (flow cytometric seed screen). Most individuals were tetraploid (93 %), while lower frequencies of hexaploid (6 %), diploid (<1 %) and triploid (<1 %) individuals were also identified. Key Results A flow cytometric analysis of 24 single seeds per individual, and five individuals per population demonstrated opposite patterns between ploidy types, with tetraploids producing more apomictic (73 %) than sexual (24 %) seed, while hexaploids produced more sexual (73 %) than apomictic (23 %) seed. As hexaploids are derived from tetraploids, these data imply that gene dosage, in addition to the effects of hybridization, influences the switch from apomictic to sexual reproduction. No significant differences in seed production were found between Europe and North America. An analysis of population structure based upon microsatellite profiling demonstrated three major genetic clusters in Europe, whose distribution was reflective of Pleistocene glaciation (e.g. refugia) and post-glacial recolonization of Europe. Conclusions The presence of pure and mixed populations representing all three genetic clusters in North America demonstrates that H. perforatum was introduced multiple times onto the continent, followed by gene flow between the different gene pools. Taken together, the data presented here suggest that plasticity in reproduction has no influence on the invasive potential of H. perforatum. PMID:24344138

  9. Perils of gene mapping with microsatellite markers

    SciTech Connect

    Knowles, J.A.; Gilliam, T.C. ); Vieland, V.J. )

    1992-10-01

    The discovery of microsatellite polymorphisms has revitalized the genetic mapping of the human genome and promises to have a dramatic effect on human disease gene mapping. The high polymorphicity, relative abundance, and amenability of these markers to assay by PCR amplification gives them a significant advantage over previous markers, which explains their general acceptance and widespread use (Litt and Luty 1989; Weber and May 1989). Preliminary chromosome maps have been constructed using microsatellites exclusively (Weber et al. 1991; Hazen et al. 1992; Kwiatkowski et al. 1992), and disease loci have been mapped by linkage to these markers (Wijmenga et al. 1991). The markers provide new optimism for the mapping of disease genes, particularly for the mapping of complex genetic disorders. The authors present evidence that the very qualities that render these markers so efficient for chromosome mapping in large reference pedigrees can lead to dramatic lod score bias when applied to the typical pedigrees used to study genetic disorders, particularly when the disorder under study is complex. 11 refs., 2 figs., 1 tab.

  10. Characterization of microsatellite markers for Baccharis dracunculifolia (Asteraceae)1

    PubMed Central

    Belini, Camila M. B.; Marques, Marcia O. M.; Figueira, Glyn M.; Bajay, Miklos M.; Campos, Jaqueline B.; Viana, João P. G.; Pinheiro, José B.; Zucchi, Maria I.

    2016-01-01

    Premise of the study: Baccharis dracunculifolia (Asteraceae) is a native plant of the Atlantic Forest that is used for the production of essential oil. Microsatellite markers were developed for this species to investigate the genetic diversity of three natural populations. Methods and Results: Seventeen out of 27 microsatellite loci identified in a genomic library used for the characterization of 315 individuals derived from three natural populations of B. dracunculifolia resulted in successful amplifications. Eleven polymorphic loci, ranging from two to seven alleles per locus, were obtained with expected and observed heterozygosity values ranging between 0.068 and 0.775 and 0.046 and 0.667, respectively. Conclusions: The microsatellite loci described in this study are tools that can be used for further studies of population genetics of B. dracunculifolia with a focus on deforested areas and conservation of natural populations. PMID:27011894

  11. Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing.

    PubMed

    Schoebel, C N; Brodbeck, S; Buehler, D; Cornejo, C; Gajurel, J; Hartikainen, H; Keller, D; Leys, M; Ríčanová, S; Segelbacher, G; Werth, S; Csencsics, D

    2013-03-01

    Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab-tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time-consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.

  12. Development of highly transferable microsatellites for Panax ginseng (Araliaceae) using whole-genome data1

    PubMed Central

    Jiang, Peng; Shi, Feng-Xue; Li, Ya-Ling; Liu, Bao; Li, Lin-Feng

    2016-01-01

    Premise of the study: Highly transferable expressed sequence tag (EST) microsatellites were developed for Panax ginseng (Araliaceae), one of the most celebrated traditional Chinese medicines and an endangered species in East Asia, using whole-genome data. Methods and Results: Twenty-one EST microsatellites were characterized from next-generation sequencing and were composed of di- and trinucleotide repeats. Polymorphisms and genetic diversity were evaluated for 45 accessions of three ginseng landraces. The number of alleles for each locus ranged from one to five among the landraces, and the polymorphism information content varied from 0.0000 to 0.6450. These microsatellites were also tested for congeneric amplification with P. notoginseng, P. stipuleanatus, P. quinquefolius, P. bipinnatifidus, and the closely related species Aralia elata. Conclusions: These novel EST-derived microsatellite markers will facilitate further population genetic studies of the genera Panax and Aralia. PMID:27843725

  13. Development and characterization of microsatellite markers in the African deciduous tree Terminalia superba (Combretaceae)1

    PubMed Central

    Demenou, Boris B.; Migliore, Jérémy; Tosso, Felicien; Kaymak, Esra; Hardy, Olivier J.

    2015-01-01

    Premise of the study: Microsatellites were designed and characterized in the African timber forest tree Terminalia superba (Combretaceae). Due to their high variability, these markers are suitable to investigate gene flow patterns and the structure of genetic diversity. Methods and Results: From a genomic library obtained by next-generation sequencing, seven monomorphic and 14 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 27 alleles (mean 11.4; expected heterozygosity range 0.283–0.940, mean 0.736) in one population from southeastern Cameroon. Genotypes were typical of an outbreeding diploid species, although null alleles explain a significant heterozygote deficit in three loci. Cross-amplification in three congeneric species (T. ivorensis, T. avicennioides, and T. mantaly) failed, suggesting that T. superba is rather divergent. Conclusions: This set of newly developed microsatellite markers will be useful for assessing the genetic diversity, population structure, and demographic history of T. superba in tropical African forests. PMID:26697276

  14. Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae)1

    PubMed Central

    Zhou, Juannan; Dudash, Michele R.; Fenster, Charles B.; Zimmer, Elizabeth A.

    2016-01-01

    Premise of the study: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. Methods and Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. virginica and S. caroliniana and were also polymorphic. Conclusions: The microsatellite markers reported here provide a valuable tool for paternity analysis in S. stellata. They will also be useful for investigating the population genetic structures of S. stellata and related species. PMID:28101439

  15. Development of microsatellite markers for the clonal shrub Orixa japonica (Rutaceae) using 454 sequencing1

    PubMed Central

    Tamaki, Ichiro; Setsuko, Suzuki; Sugai, Kyoko; Yanagisawa, Nao

    2016-01-01

    Premise of the study: Microsatellite markers were developed for a dioecious shrub, Orixa japonica (Rutaceae). Because O. japonica vigorously propagates by vegetative growth, microsatellite markers can be used to identify clonal relationships among its ramets. Methods and Results: Sixteen polymorphic microsatellite markers were identified by 454 next-generation sequencing. The number of alleles and expected heterozygosity for each locus among four populations ranged from two to 10 and from 0.140 to 0.875, respectively. Five of the 16 loci showed a low null allele frequency. Because Orixa is a monotypic genus, cross-amplification in a consubfamilial species, Skimmia japonica, was tested, and only one locus showed polymorphism. Conclusions: These microsatellite markers developed for O. japonica contribute to clone identification for studies examining the clonal structure and true sex ratio in the wild. Moreover, five markers that have a low null allele frequency can also be used for estimating mating systems or performing parentage analysis. PMID:27785383

  16. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    NASA Astrophysics Data System (ADS)

    Li, Li; Guo, Ximing; Zhang, Guofan

    2009-02-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  17. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species1

    PubMed Central

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M. Iqbal; Zerega, Nyree J. C.

    2013-01-01

    • Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit. PMID:25202565

  18. Development of a novel set of microsatellite markers for Lippia alba (Verbenaceae).

    PubMed

    Rocha, D S; Santos, C P; Bajay, M M; Campos, J B; Blank, A F; Pinheiro, J B; Zucchi, M I

    2015-02-03

    Microsatellite primers were developed and optimized for Lippia alba to characterize the L. alba germplasm bank of Universidade de São Paulo. A genomic library enabled the design of 9 microsatellite primers. Six of the 9 primers yielded polymorphic products, which defined 2 groups in the bank. The data provide support to characterize germplasm banks, genetic breeding programs for L. alba, and other genetic diversity studies and classifications of species in the genus Lippia.

  19. Design and Implementation of Degenerate Microsatellite Primers for the Mammalian Clade

    PubMed Central

    Buschiazzo, Emmanuel; Beck, Josephine S.; Gemmell, Neil J.

    2011-01-01

    Microsatellites are popular genetic markers in molecular ecology, genetic mapping and forensics. Unfortunately, despite recent advances, the isolation of de novo polymorphic microsatellite loci often requires expensive and intensive groundwork. Primers developed for a focal species are commonly tested in a related, non-focal species of interest for the amplification of orthologous polymorphic loci; when successful, this approach significantly reduces cost and time of microsatellite development. However, transferability of polymorphic microsatellite loci decreases rapidly with increasing evolutionary distance, and this approach has shown its limits. Whole genome sequences represent an under-exploited resource to develop cross-species primers for microsatellites. Here we describe a three-step method that combines a novel in silico pipeline that we use to (1) identify conserved microsatellite loci from a multiple genome alignments, (2) design degenerate primer pairs, with (3) a simple PCR protocol used to implement these primers across species. Using this approach we developed a set of primers for the mammalian clade. We found 126,306 human microsatellites conserved in mammalian aligned sequences, and isolated 5,596 loci using criteria based on wide conservation. From a random subset of ∼1000 dinucleotide repeats, we designed degenerate primer pairs for 19 loci, of which five produced polymorphic fragments in up to 18 mammalian species, including the distinctly related marsupials and monotremes, groups that diverged from other mammals 120–160 million years ago. Using our method, many more cross-clade microsatellite loci can be harvested from the currently available genomic data, and this ability is set to improve exponentially as further genomes are sequenced. PMID:22216321

  20. Isolation and characterization of microsatellite markers for an endemic tree in East Asia, Quercus variabilis (Fagaceae)1

    PubMed Central

    Wang, Xian; Li, Jing; Li, Yong

    2015-01-01

    Premise of the study: Microsatellite markers of Quercus variabilis (Fagaceae) were isolated for population genetic and landscape genetic studies. Methods and Results: Roche 454 pyrosequencing combined with the magnetic bead enrichment protocol were used to isolate microsatellite markers for Q. variabilis. A total of 2121 microsatellites were identified from 63,851 individual sequence reads. One hundred microsatellite loci were selected to test primer amplification efficiency among 24 individuals from two wild populations. Among the 100 tested markers, 34 primer pairs were successfully amplified. Of these, 14 yielded polymorphic amplification products, whereas the remaining 20 loci were monomorphic. The number of alleles for polymorphic loci ranged from two to six, and the observed heterozygosity ranged from 0.042 to 0.750. Conclusions: These microsatellite loci will provide useful tools for further population genetic and landscape genetic studies on Q. variabilis. PMID:26082882

  1. Ploidy, sex and crossing over in an evolutionary aging model

    NASA Astrophysics Data System (ADS)

    Lobo, Matheus P.; Onody, Roberto N.

    2006-02-01

    Nowadays, many forms of reproduction coexist in nature: Asexual, sexual, apomictic and meiotic parthenogenesis, hermaphroditism and parasex. The mechanisms of their evolution and what made them successful reproductive alternatives are very challenging and debated questions. Here, using a simple evolutionary aging model, we give a possible scenario. By studying the performance of populations where individuals may have diverse characteristics-different ploidies, sex with or without crossing over, as well as the absence of sex-we find an evolution sequence that may explain why there are actually two major or leading groups: Sexual and asexual. We also investigate the dependence of these characteristics on different conditions of fertility and deleterious mutations. Finally, if the primeval organisms on Earth were, in fact, asexual individuals we conjecture that the sexual form of reproduction could have more easily been set and found its niche during a period of low-intensity mutations.

  2. Microsatellites Cross-Species Amplification across Some African Cichlids.

    PubMed

    Bezault, Etienne; Rognon, Xavier; Gharbi, Karim; Baroiller, Jean-Francois; Chevassus, Bernard

    2012-01-01

    The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P(95)) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.

  3. Reference cells and ploidy in the comet assay.

    PubMed

    Brunborg, Gunnar; Collins, Andrew; Graupner, Anne; Gutzkow, Kristine B; Olsen, Ann-Karin

    2015-01-01

    In the comet assay single cells are analyzed with respect to their level of DNA damage. Discrimination of the individual cell or cell type based on DNA content, with concomitant scoring of the DNA damage, is useful since this may allow analysis of mixtures of cells. Different cells can then be characterized based on their ploidy, cell cycle stage, or genome size. We here describe two applications of such a cell type-specific comet assay: (i) Testicular cell suspensions, analyzed on the basis of their ploidy during spermatogenesis; and (ii) reference cells in the form of fish erythrocytes which can be included as internal standards to correct for inter-assay variations. With standard fluorochromes used in the comet assay, the total staining signal from each cell - whether damaged or undamaged - was found to be associated with the cell's DNA content. Analysis of the fluorescence intensity of single cells is straightforward since these data are available in scoring systems based on image analysis. The analysis of testicular cell suspensions provides information on cell type specific composition, susceptibility to genotoxicants, and DNA repair. Internal reference cells, either untreated or carrying defined numbers of lesions induced by ionizing radiation, are useful for investigation of experimental factors that can cause variation in comet assay results, and for routine inclusion in experiments to facilitate standardization of methods, and comparison of comet assay data obtained in different experiments or in different laboratories. They can also be used - in combination with a reference curve - to quantify the DNA lesions induced by a certain treatment. Fish cells of a range of genome sizes, both greater and smaller than human, are suitable for this purpose, and they are inexpensive.

  4. Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats

    PubMed Central

    Driscoll, Carlos A.; Menotti-Raymond, Marilyn; Nelson, George; Goldstein, David; O'Brien, Stephen J.

    2002-01-01

    Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000–17,000 yr ago), and in Asiatic lions of the Gir Forest (1000–4000 yr ago). [Supplemental material available online at http://rex.nci.nih.gov/lgd/front_page.htm and at http://www.genome.org.] PMID:11875029

  5. Genomic microsatellites as evolutionary chronometers: a test in wild cats.

    PubMed

    Driscoll, Carlos A; Menotti-Raymond, Marilyn; Nelson, George; Goldstein, David; O'Brien, Stephen J

    2002-03-01

    Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000-17,000 yr ago), and in Asiatic lions of the Gir Forest (1000-4000 yr ago).

  6. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Pedraza, F; Buendia, H F; Gaitán-Solís, E; Beebe, S E; Gepts, P; Tohme, J

    2003-11-01

    A total of 150 microsatellite markers developed for common bean ( Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican x Andean population, DOR364 x G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two inter-genepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.

  7. Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers.

    PubMed Central

    Lench, N J; Norris, A; Bailey, A; Booth, A; Markham, A F

    1996-01-01

    We have developed a vectorette PCR approach to provide an improved method for isolation of microsatellite repeats. The modified procedure relies on PCR amplification using a vectorette-specific primer in combination with one of a panel of anchored dinucleotide repeat primers. The target DNA to be screened for microsatellite sequences can be from YAC, P1, cosmid, bacteriophage or plasmid clones. We have used this technique to isolate novel, polymorphic microsatellite repeats from clones containing the amelogenin gene (AMGX) located on human chromosome Xp22.3. PMID:8668553

  8. Microsatellite primers in the lichen symbiotic alga Trebouxia decolorans (Trebouxiophyceae)1

    PubMed Central

    Dal Grande, Francesco; Beck, Andreas; Singh, Garima; Schmitt, Imke

    2013-01-01

    • Premise of the study: Polymorphic microsatellite markers were developed for the symbiotic green alga Trebouxia decolorans to study fine-scale population structure and clonal diversity. • Methods and Results: Using Illumina pyrosequencing, 20 microsatellite primer sets were developed for T. decolorans. The primer sets were tested on 43 individuals sampled from four subpopulations in Germany. The primers amplified di-, tri-, and tetranucleotide repeats with three to 15 alleles per locus, and the unbiased haploid diversity per locus ranged from 0.636 to 0.821. • Conclusions: The identified microsatellite markers will be useful to study the genetic diversity, dispersal, and reproductive mode of this common lichen photobiont. PMID:25202529

  9. Characterization of microsatellite DNA markers for the alligator snapping turtle, Macrochelys temminckii: Primer note

    USGS Publications Warehouse

    Hackler, J.C.; Van Den Bussche, Ronald A.; Leslie, David M.

    2007-01-01

    Two trinucleotide and seven tetranucleotide microsatellite loci were isolated from an alligator snapping turtle Macrochelys temminckii. To assess the degree of variability in these nine microsatellite loci, we genotyped 174 individuals collected from eight river drainage basins in the southeastern USA. These markers revealed a moderate degree of allelic diversity (six to 16 alleles per locus) and observed heterozygosity (0.166-0.686). These polymorphic microsatellite loci provide powerful tools for population genetic studies for a species that is afforded some level of conservation protection in every state in which it occurs. ?? 2006 The Authors.

  10. Development of novel microsatellite markers for strain-specific identification of Chlorella vulgaris.

    PubMed

    Jo, Beom-Ho; Lee, Chang Soo; Song, Hae-Ryong; Lee, Hyung-Gwan; Oh, Hee-Mock

    2014-09-01

    A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

  11. Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines.

    PubMed

    González-Martínez, S C; Robledo-Arnuncio, J J; Collada, C; Díaz, A; Williams, C G; Alía, R; Cervera, M T

    2004-06-01

    Microsatellite transfer across coniferous species is a valued methodology because de novo development for each species is costly and there are many species with only a limited commodity value. Cross-species amplification of orthologous microsatellite regions provides valuable information on mutational and evolutionary processes affecting these loci. We tested 19 nuclear microsatellite markers from Pinus taeda L. (subsection Australes) and three from P. sylvestris L. (subsection Pinus) on seven Eurasian hard pine species ( P. uncinata Ram., P. sylvestris L., P. nigra Arn., P. pinaster Ait., P. halepensis Mill., P. pinea L. and P. canariensis Sm.). Transfer rates to species in subsection Pinus (36-59%) were slightly higher than those to subsections Pineae and Pinaster (32-45%). Half of the trans-specific microsatellites were found to be polymorphic over evolutionary times of approximately 100 million years (ten million generations). Sequencing of three trans-specific microsatellites showed conserved repeat and flanking regions. Both a decrease in the number of perfect repeats in the non-focal species and a polarity for mutation, the latter defined as a higher substitution rate in the flanking sequence regions close to the repeat motifs, were observed in the trans-specific microsatellites. The transfer of microsatellites among hard pine species proved to be useful for obtaining highly polymorphic markers in a wide range of species, thereby providing new tools for population and quantitative genetic studies.

  12. Characterization and cross-species amplification of microsatellite markers in African Silverbill (Lonchura cantans).

    PubMed

    Parine, N R; Kumar, D; Pathan, A A K; Elrobh, M S; Khan, W; Alanazi, M

    2013-11-18

    We tested the cross-amplification of eight microsatellites developed for Bengalese finch in African Silverbill (Lonchura cantans). In order to develop resources for conservation genetic studies in the species L. cantans, we tested the amplification success and polymorphism in eight previously developed microsatellite loci, in L. cantans. All eight microsatellite markers were successfully amplified, of which all were polymorphic, with 3 to 9 alleles and an expected heterozygosity (HE) ranging from 0.606 to 0.718. On average, there were 5.25 alleles/locus and a mean HE of 0.6456. These eight polymorphic markers could be of potential use in studies of genetic variability, population structure, and reproductive strategy of African Silverbills. The markers tested should be useful for population and conservation genetic studies in this genus, and, in particular, for species closely related to the source species, L. cantans.

  13. The coordination of ploidy and cell size differs between cell layers in leaves

    PubMed Central

    Katagiri, Yohei; Hasegawa, Junko; Fujikura, Ushio; Hoshino, Rina; Matsunaga, Sachihiro; Tsukaya, Hirokazu

    2016-01-01

    Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell differentiation. Here, we report that the level of correlation between ploidy and cell volume is different in the outer and inner cell layers of leaves of Arabidopsis thaliana using a novel imaging technique. Although there is a well-known, strong correlation between ploidy and cell volume in pavement cells of the epidermis, this correlation was extremely weak in palisade mesophyll cells. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells. We therefore propose that the correlation between ploidy and cell volume is regulated by cell identity. PMID:26903507

  14. Image cytometry determination of ploidy level, proliferative activity, and nuclear size in a series of 314 transitional bladder cell carcinomas.

    PubMed

    van Velthoven, R; Petein, M; Oosterlinck, W J; Zandona, C; Zlotta, A; Van der Meijden, A P; Pasteels, J L; Roels, H; Schulman, C; Kiss, R

    1995-01-01

    Image cytometry was carried out on 281 superficial (Ta and T1) and 33 invasive (T2 to T4) bladder cancers. The parameters used to characterize these bladder tumors were: (1) histopathological grading, (2) clinical staging, (3) tumor size, (4) deoxyribonucleic acid (DNA) index (DI), (5) DNA histogram type (DHT), (6) percentage of euploid (diploid plus tetraploid) cells, (7) percentage of polyploid cells (> 5C DNA content), (8) proliferative activity (S phase fraction value), and (9) nuclear area (NA). The proliferative activity of the tumors was not related to either histopathological grade or to clinical stage, but it was related to the DHT parameter, which made it possible to identify diploid, hyperdiploid, triploid, hypertriploid, tetraploid, and polymorphic tumors. The hypertriploid tumors exhibited a significantly lower proliferative activity than the nonhypertriploid ones. Although both the DI and the NA values correlated significantly with histopathological grading, only the NA values correlated significantly with clinical staging. We further observed that some grade III bladder tumors were definitely diploid, whereas some grade I tumors were highly aneuploid. We thus hypothesize that the ploidy level of a given tumor reflects its age directly and its aggressiveness only very indirectly. In our opinion aneuploidy is only an indirect marker of aggressiveness because it reflects the fact that a malignant tumor is old, ie, has been present in a patient over a long period of time and has had ample time to express its malignancy at the clinical level. A significant relationship was accordingly obtained between tumor size and ploidy level with the highest proportion of aneuploid tumors and the highest percentage of polyploid cell nuclei being observed among the largest bladder tumors.

  15. Characterization of microsatellite DNA libraries from three mealybug species and development of microsatellite markers for Pseudococcus viburni (Hemiptera: Pseudococcidae).

    PubMed

    Correa, M C G; Zaviezo, T; Le Maguet, J; Herrbach, E; Malausa, T

    2014-04-01

    Mealybugs (Hemiptera: Pseudococcidae) are important pests for crops worldwide. Different species, cryptic taxa under the same species name or even populations within a species can differ in biological characteristics, such as phenology, resistance to insecticides, virus transmission and susceptibility to natural enemies. Therefore, their management efficacy depends on their accurate identification. Microsatellite genetic markers are efficient in revealing the fine-scale taxonomic status of insects, both at inter- and intra-specific level. Despite their potential uses, microsatellites have been developed only for one mealybug species so far. Hence, it is unclear whether microsatellites may be useful to assess mealybug population differentiation and structuring. In this work, we tested the feasibility of developing microsatellite markers in mealybugs by: (i) producing and characterizing microsatellite DNA libraries for three species: Pseudococcus viburni, Pseudococcus comstocki and Heliococcus bohemicus, and (ii) by developing and testing markers for Ps. viburni. The obtained libraries contained balanced percentages of dinucleotide (ranging from 15 to 25%) and trinucleotide (from 5 to 17%) motifs. The marker setup for Ps. viburni was successful, although 70% of the primers initially tested were discarded for a lack of polymorphism. Finally, 25 markers were combined in two multiplex polymerase chain reactions with 21 displaying no evidence of deviation from Hardy-Weinberg equilibrium. Ps. viburni markers were tested on one population from France and one from Chile. The markers revealed a significant genetic differentiation between the two populations with an Fst estimate of 0.266.

  16. Microsatellite markers isolated from the flightless cormorant (Phalacrocorax harrisi).

    PubMed

    Duffie, Caroline; Glenn, Travis C; Hagen, Cris; Parker, Patricia

    2008-05-01

    Eight polymorphic microsatellite DNA loci were isolated from the flightless cormorant (Phalacrocorax harrisi) for future population genetic studies. Genetic variability was assessed using at least 38 individuals from two populations. Allele numbers ranged from three to nine per locus. Mean observed heterozygosity varied from 0.27 to 0.78. No locus deviated from Hardy-Weinberg (HW) or linkage equilibria in either population. The high levels of detected polymorphism indicate the utility of these markers for population genetic studies of this Galápagos species.

  17. Rangewide ploidy variation and evolution in Acacia senegal: a north–south divide?

    PubMed Central

    Odee, David W.; Wilson, Julia; Omondi, Stephen; Perry, Annika; Cavers, Stephen

    2015-01-01

    Knowledge of rangewide variation in DNA content and ploidy level may be valuable in understanding the evolutionary history of a species. Recent studies of Acacia senegal report diploids and occasional tetraploids in the Sudano-Sahelian region of sub-Saharan Africa, but nothing is known about the overall extent of DNA ploidy variation within the species. In this study, we determine the DNA content and ploidy level of A. senegal across its native range, and explore whether the variation is related to its evolutionary and colonization history. We used propidium iodide flow cytometry (FCM) to estimate DNA content (2C value) and infer ploidy in 157 individuals from 54 populations on various tissues, using seeds, fresh leaves, dried leaves and twigs and herbarium specimens. The mean 2C DNA (pg ± s.d.) contents detected were 1.47 ± 0.09, 2.12 ± 0.02, 2.89 ± 0.12, and a single individual with 4.51 pg, corresponding to a polyploid series of diploid, triploid, tetraploid and hexaploid individuals. Diploids were confirmed by chromosome counts (2n = 2x = 26). Most populations (90.7 %) were of single ploidy level, while mixed ploidy populations (9.3 %) comprising mostly diploids (2x+3x, 2x+4x and 2x+6x) were restricted to the Sudano-Sahelian and Indian subcontinent regions, its northern range. The species is predominantly diploid, and no mixed ploidy populations were detected in east and southern Africa, its southern range. The geographic pattern of ploidy variation in conjunction with existing phylogeographic and phylogenetic data of the species suggests that polyploids have occurred multiple times in its evolutionary and recent colonization history, including contemporary ecological timescales. The successful use of external tissues of dried twigs in FCM is new, and presents the opportunity to study numerous other dryland woody species. PMID:25680798

  18. Development of microsatellite markers in Cratylia mollis and their transferability to C. argentea (Fabaceae)1

    PubMed Central

    López-Roberts, M. Cristina; de Queiroz, Luciano Paganucci; van den Berg, Cássio

    2013-01-01

    • Premise of the study: This work aimed to develop microsatellite markers for Cratylia mollis as tools to assess its genetic diversity and structure and to evaluate their potential cross-amplification in related species. • Methods and Results: Microsatellite markers were developed using a microsatellite-enriched library and an intersimple sequence repeat library. From a set of 19 markers, 12 microsatellite loci were polymorphic and presented considerable variation in allele number (2–11), expected heterozygosity (0.226–0.883), and polymorphism information content per locus (0.212–0.870). Cross-amplification in C. argentea was successful in 16 loci, 12 of which were polymorphic (2–10 alleles). • Conclusions: The polymorphism of this set of microsatellite markers for C. mollis, as well as their successful cross-amplification in C. intermedia and C. bahiensis and their transferability to C. argentea, supports their use in future comparative studies to understand the mechanism involved in population divergence and speciation in the genus. PMID:25202484

  19. Student's Microsatellite Project

    NASA Astrophysics Data System (ADS)

    Zelentsov, Victor; Kopik, Anatoliy; Karpenko, Stanislav; Mayorova, Victoria

    2002-01-01

    Nowadays BMSTU Youth space center carries on development of the microsatellite project. The project is based on principles of students direct involvement on all stages of development and maintenance of the satellite. The group of students was organized within the university with purpose of coordination of work at the program. Project current condition The work on creation of an experimental model of the micro satellite is performed. The aim is to define the structure and parameters of on-board devices (mass-overall dimensions characteristics, energy consumption and so on). developed. According to the simplified model an active stabilization system (three orthogonal electro-magnetic coils) and orientation characterization system (sunlight detector and magnitometer) are included in OCS structure. most suitable battery storage, power-supply controlling system. Student micro-satellite program goals 1.Scientific Information gaining in the field of Earth study- using perspective research methods. Studying of new devices behavior in space conditions. 2. Educative a. Students derive real experience of projecting, building of a spacecraft from the point of view of an experimenter, a constructor and a researcher. b. Organization of student's cooperation with key men of aerospace industry and other branches. c. Brainpower and material base preparation for micro-satellite systems' development. d. Attraction of youth interest to the topic, by: - Students' and pupils' groups attraction and involvement in experiments conduction and results processing. - Seminars and lections devoted to Earth study from the space organization - Specific scientific data distribution over World Wide Web. 3. International With purpose of program expansion, the developers' group looks to start of an international project. Within the project new experiments conduction and scientific information exchange are expected. 4. Status Bauman Moscow State Technical University's status improvement in the field

  20. Clinical application of DNA ploidy to cervical cancer screening: A review

    PubMed Central

    Garner, David

    2014-01-01

    Screening for cervical cancer with DNA ploidy assessment by automated quantitative image cytometry has spread throughout China over the past decade and now an estimated 1 million tests per year are done there. Compared to conventional liquid based cytology, DNA ploidy has competitive accuracy with much higher throughput per technician. DNA ploidy has the enormous advantage that it is an objective technology that can be taught in typically 2 or 3 wk, unlike qualitative cytology, and so it can enable screening in places that lack sufficient qualified cytotechnologists and cytopathologists for conventional cytology. Most papers on experience with application of the technology to cervical cancer screening over the past decade were published in the Chinese language. This review aims to provide a consistent framework for analysis of screening data and to summarize some of the work published from 2005 to the end of 2013. Of particular interest are a few studies comparing DNA ploidy with testing for high risk human papilloma virus (hrHPV) which suggest that DNA ploidy is at least equivalent, easier and less expensive than hrHPV testing. There may also be patient management benefits to combining hrHPV testing with DNA ploidy. Some knowledge gaps are identified and some suggestions are made for future research directions. PMID:25493231

  1. Genome ploidy in different stages of the Giardia lamblia life cycle.

    PubMed

    Bernander, R; Palm, J E; Svärd, S G

    2001-01-01

    The early diverging eukaryotic parasite Giardia lamblia is unusual in that it contains two apparently identical nuclei in the vegetative trophozoite stage. We have determined the nuclear and cellular genome ploidy of G. lamblia cells during all stages of the life cycle. During vegetative growth, the nuclei cycle between a diploid (2N) and tetraploid (4N) genome content and the cell, consequently, cycles between 4N and 8N. Stationary phase trophozoites arrest in the G2 phase with a ploidy of 8N (two nuclei, each with a 4N ploidy). On its way to cyst formation, a G1 trophozoite goes through two successive rounds of chromosome replication without an intervening cell division event. Fully differentiated cysts contain four nuclei, each with a ploidy of 4N, resulting in a cyst ploidy of 16N. The newly excysted cell, for which we suggest the term 'excyzoite', contains four nuclei (cellular ploidy 16N). In a reversal of the events occurring during encystation, the excyzoite divides twice to form four trophozoites containing two diploid nuclei each. The formation of multiple cells from a single cyst is likely to be one of the main reasons for the low infectious doses of G. lamblia.

  2. Driven apart: the evolution of ploidy differences between the sexes under antagonistic selection.

    PubMed

    Immler, Simone; Otto, Sarah Perin

    2014-01-01

    Sexual reproduction in eukaryotes implies a biphasic life cycle with alternating haploid and diploid phases. The nature of the biphasic life cycle varies markedly across taxa, and often either the diploid or the haploid phase is predominant. Why some taxa spend a major part of their life cycle as diploids and others as haploids remains a conundrum. Furthermore, ploidy levels may not only vary across life cycle phases but may also differ between males and females. The existence of two life cycle phases and two sexes bears a high potential for antagonistic selection, which in turn may influence the evolution of ploidy levels. We explored the evolution of ploidy levels when selection depends on both ploidy and sex. Our analyses show that antagonistic selection may drive the ploidy levels between males and females apart. In a subsequent step, we explicitly explored the evolution of arrhenotoky (i.e., haploid males and diploid females) in the context of antagonistic selection. Our model shows that selection on arrhenotoky depends on male fitness but evolves regardless of the fitness consequences to females. Overall we provide a plausible explanation for the evolution of sex differences in ploidy levels, a principle that can be extended to any system with asymmetric inheritance.

  3. Microsatellite markers in the western prairie fringed orchid, Platanthera praeclara (Orchidaceae)1

    PubMed Central

    Ross, Andrew A.; Aldrich-Wolfe, Laura; Lance, Stacey; Glenn, Travis; Travers, Steven E.

    2013-01-01

    • Premise of the study: Primers for 31 microsatellite-containing loci were developed for the threatened orchid Platanthera praeclara to enable characterization of the population genetics of this tallgrass prairie native. • Methods and Results: Sixteen polymorphic microsatellite loci were identified from four populations. Six of these loci were not in linkage disequilibrium. The average number of alleles per locus per population ranged from 6.4 to 8.9. • Conclusions: The results indicate that six of the polymorphic loci will be useful in future studies of population structure, gene flow, and genetic diversity. PMID:25202536

  4. Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

    USGS Publications Warehouse

    Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

    2009-01-01

    In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

  5. Enhanced cross-species utility of conserved microsatellite markers in shorebirds

    PubMed Central

    Küpper, Clemens; Burke, Terry; Székely, Tamás; Dawson, Deborah A

    2008-01-01

    Background Microsatellite markers are popular genetic markers frequently used in forensic biology. Despite their popularity, the characterisation of polymorphic microsatellite loci and development of suitable markers takes considerable effort. Newly-available genomic databases make it feasible to identify conserved genetic markers. We examined the utility and characteristics of conserved microsatellite markers in Charadriiformes (plovers, sandpipers, gulls and auks). This order harbours many species with diverse breeding systems, life histories and extraordinary migration biology whose genetics warrant investigation. However, research has been largely restrained by the limited availability of genetic markers. To examine the utility of conserved microsatellite loci as genetic markers we collated a database of Charadriiformes microsatellites, searched for homologues in the chicken genome and tested conserved markers for amplification and polymorphism in a range of charadriiform species. Results Sixty-eight (42%) of 161 charadriiform microsatellite loci were assigned to a single location in the chicken genome based on their E-value. Fifty-five primers designed from conserved microsatellite loci with an E-value of E-10 or lower amplified across a wider range of charadriiform species than a control group of primers from ten anonymous microsatellite loci. Twenty-three of 24 examined conserved markers were polymorphic, each in on average 3 of 12 species tested. Conclusion Genomic sequence databases are useful tools to identify conserved genetic markers including those located in non-coding regions. By maximising primer sequence similarity between source species and database species, markers can be further improved and provide additional markers to study the molecular ecology of populations of non-model organisms. PMID:18950482

  6. The Microgeographical Patterns of Morphological and Molecular Variation of a Mixed Ploidy Population in the Species Complex Actinidia chinensis

    PubMed Central

    Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

    2015-01-01

    Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches. PMID:25658107

  7. Analyses of phenotype and ARGOS and ASY1 expression in a ploidy Chinese cabbage series derived from one haploid.

    PubMed

    Gu, Ai Xia; Zhao, Jian Jun; Li, Li Min; Wang, Yan Hua; Zhao, Yu Jing; Hua, Fan; Xu, Yuan Chao; Shen, Shu Xing

    2016-03-01

    The aim of this research was to improve our understanding of how ploidy level influences phenotype and gene expression in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Haploid plants (2n = 10) was induced by 0.2% colchicine to produce diploid (2n = 20) and tetraploid plants (2n = 40). The aneuploid (2n = 24) was also obtained by hybridization between diploid plants as the female and tetraploid plants. The ploidy levels of all plants were identified through chromosome counts and flow cytometry. Leaves and petals became larger as the ploidy level increased from haploid to diploid, and from aneuploid to tetraploid. Similarly, expression of ARGOS was regulated by genome size, increasing in parallel with the level of ploidy. Among the four ploidy types, expression was stronger in the floral buds than in the leaves. Expression by ASY1 also differed according to ploidy level, being highest in diploid plants, followed in order by tetraploids. Expression was similar between haploids and aneuploids at two stages-prior to and after meiosis-but was higher in the haploids during meiosis. When buds were compared within the same ploidy type at different stages, ASY1 expression was obviously higher during meiosis than either before or after. Our study demonstrated the generation and phenotype of a ploidy Chinese cabbage series derived from one haploid. Expression of genes ARGOS and ASY1 were modulated by genome size in this ploidy series, and the regulated patterns of the two genes was different.

  8. Development of microsatellite loci of pod mahogany, Afzelia quanzensis (Fabaceae), by Illumina shotgun sequencing, and cross-amplification in A. africana1

    PubMed Central

    Jinga, Percy; Palagi, Jason; Ashley, Mary V.

    2016-01-01

    Premise of the study: Microsatellite loci were developed for Afzelia quanzensis (Fabaceae) as a first step toward investigating genetic diversity and population structure of the species in its native range. Methods and Results: Illumina shotgun sequencing was used to generate raw sequence reads, which were searched for potential microsatellite loci. A total of 70 potential microsatellite loci were tested for amplification and polymorphism, and 39 successfully amplified. Of the 39 loci that amplified, 12 were polymorphic while 27 were monomorphic. The 12 polymorphic loci were cross-amplified in A. africana, and eight successfully amplified. Conclusions: The 12 polymorphic microsatellite loci can be used for genetic studies of A. quanzensis, which can help determine its conservation status. Eight loci can also be used for genotyping in A. africana. PMID:27347453

  9. Hybrid speciation in angiosperms: parental divergence drives ploidy

    PubMed Central

    Paun, Ovidiu; Forest, Félix; Fay, Michael F.; Chase, Mark W.

    2010-01-01

    Summary Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (i.e. as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed. PMID:19220761

  10. Bridging global and microregional scales: ploidy distribution in Pilosella echioides (Asteraceae) in central Europe

    PubMed Central

    Trávníček, Pavel; Dočkalová, Zuzana; Rosenbaumová, Radka; Kubátová, Barbora; Szeląg, Zbigniew; Chrtek, Jindřich

    2011-01-01

    Background and Aims A detailed knowledge of cytotype distribution can provide important insights into the evolutionary history of polyploid systems. This study aims to explore the spatial distribution of different cytotypes in Pilosella echioides at various spatial scales (from the whole distributional range to the population level) and to outline possible evolutionary scenarios for the observed geographic pattern. Methods DNA-ploidy levels were estimated using DAPI flow cytometry in 4410 individuals of P. echioides from 46 populations spread over the entire distribution range in central Europe. Special attention was paid to the cytotype structure in the most ploidy-diverse population in south-west Moravia. Key Results Five different cytotypes (2x, 3x, 4x, 5x and 6x) were found, the last being recorded for the first time. Although ploidy-uniform (di- or tetraploid) sites clearly prevailed, nearly one-quarter of the populations investigated harboured more (up to all five) cytotypes. Whereas penta- and hexaploids constituted only a minority of the samples, a striking predominance of the triploid cytotype was observed in several populations. Conclusions The representative sampling confirmed previous data on cytotype distribution, i.e. the spatial aggregation of mixed-ploidy populations in south-west Moravia and Lower Austria and the predominance of ploidy-uniform populations in other parts of the area investigated. Recurrent origin of polyploids from diploid progenitors via unreduced gametes and their successful establishment are considered the key factors promoting intrapopulational ploidy mixture (‘primary hybrid zones’). As an alternative to the generally accepted theory of cytotype co-existence based on the development of different means of inter-ploidy reproductive isolation, it is suggested that a long-term ploidy mixture can also be maintained in free-mating populations provided that the polyploids originate with a sufficient frequency. In addition, the

  11. Sensitivity to phosphorus limitation increases with ploidy level in a New Zealand snail.

    PubMed

    Neiman, Maurine; Kay, Adam D; Krist, Amy C

    2013-05-01

    Evolutionary and ecological factors that explain natural variation in ploidy level remain poorly understood. One intriguing possibility is that nutrient costs associated with higher per-cell nucleic acid content could differentially influence the fitness of different ploidy levels. Here, we test this hypothesis by determining whether access to phosphorus (P), a main component of nucleic acids, differentially affects growth rate in asexual freshwater snails (Potamopyrgus antipodarum) that differ in ploidy. As expected if larger genomes generate higher dietary P requirements, tetraploid P. antipodarum experienced a more than twofold greater reduction in growth rate in low-P versus high-P conditions relative to triploids. Mirroring these results, tetraploid P. antipodarum also had a significant reduction in body P content under low P relative to high P, whereas triploid body P content was unaffected. Taken together, these results set the stage for the possibility that P availability could influence the distribution and relative frequency of P. antipodarum of different ploidy levels. These findings could be applicable to many other animal taxa featuring ploidy-level variation, which includes many mixed sexual/asexual taxa.

  12. Genotyping of mature trees of Entandrophragma cylindricum with microsatellites.

    PubMed

    Garcia, F; Noyer, J-L; Risterucci, A-M; Chevallier, M-H

    2004-01-01

    We have characterized 10 microsatellite loci for the tropical tree Entandrophragma cylindricum (Sprague) Sprague (sapelli) in order to genotype individuals in forest stands for estimation of the genetic diversity of the species. We used the technique of building a (GA)n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 186 mature trees in a selectively logged stand (Dimako) and an unlogged stand (Ndama), both in Cameroon. All the loci were polymorphic, and the number of alleles was high, ranging from eight to 36, with a mean of 22.1. Both stands showed the same high level of genetic diversity (mean H(E) = 0.85) and a low genetic differentiation (FST = 0.007), indicating that genetic diversity was within rather than among populations. Five and three out seven loci in Dimako and Ndama, respectively, showed a deficit of heterozygotes. The seven loci enabled more than 97% of the mature trees in each stand to be identified. It was concluded that these markers can be efficiently used for gene flow studies.

  13. PCR primers for microsatellite loci in the desert tortoise (Gopherus agassizii, Testudinidae)

    USGS Publications Warehouse

    Edwards, T.; Goldberg, C.S.; Kaplan, M.E.; Schwalbe, C.R.; Swann, D.E.

    2003-01-01

    The desert tortoise, Gopherus agassizii, is a threatened species native to the North American desert southwest and is recognized as having distinct Mojave and Sonoran populations. We identified six polymorphic microsatellite loci in the desert tortoise. All six loci were polymorphic in Sonoran samples. Five of the loci were variable in Mojave samples with varying degrees of amplification success. Two of the loci exhibited low allelic variation (2-3 alleles) while four were highly variable (8-27 alleles).

  14. Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata.

    PubMed

    Côrtes, M C; Gowda, V; Kress, W J; Bruna, E M; Uriarte, M

    2009-07-01

    We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.

  15. Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers.

    PubMed

    Betto-Colliard, C; Sermier, R; Litvinchuk, S; Perrin, N; Stöck, M

    2015-03-01

    Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates.

  16. Microsatellite loci from the endemic Southern Ocean octopus Adelieledone polymorpha (Robson, 1930).

    PubMed

    Strugnell, Jan M; Allcock, A Louise; Watts, Phillip C

    2009-05-01

    To determine the pattern of spatial genetic structure in the endemic Southern Ocean octopus Adelieledone polymorpha, microsatellite loci were isolated from partial genomic libraries enriched for repetitive DNA motifs. Seven dinucleotide and two trinucleotide microsatellite loci were isolated successfully and levels of polymorphism were quantified in 34 individuals sampled from the Southern Ocean near South Georgia. No pairs of microsatellite loci were linked significantly; however, one locus deviated (P < 0.05) from Hardy-Weinberg equilibrium. Overall, the nine loci produced between five and 16 alleles, with observed and expected heterozygosities varying between 0.22 and 0.86 and between 0.21 and 0.94 respectively. This is the first description of microsatellite loci from an octopus endemic to the Southern Ocean, and these genetic markers are being used to quantify spatial structure within A. polymorpha.

  17. WebSat ‐ A web software for microsatellite marker development

    PubMed Central

    Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

    2009-01-01

    Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

  18. Isolation and characterization of microsatellite markers for Jasminum sambac (Oleaceae) using Illumina shotgun sequencing1

    PubMed Central

    Li, Yong; Zhang, Weirui

    2015-01-01

    Premise of the study: Microsatellite markers of Jasminum sambac (Oleaceae) were isolated to investigate wild germplasm resources and provide markers for breeding. Methods and Results: Illumina sequencing was used to isolate microsatellite markers from the transcriptome of J. sambac. A total of 1322 microsatellites were identified from 49,772 assembled unigenes. One hundred primer pairs were randomly selected to verify primer amplification efficiency. Out of these tested primer pairs, 31 were successfully amplified: 18 primer pairs yielded a single allele, seven exhibited fixed heterozygosity with two alleles, and only six displayed polymorphisms. Conclusions: This study obtained the first set of microsatellite markers for J. sambac, which will be helpful for the assessment of wild germplasm resources and the development of molecular marker–assisted breeding. PMID:26504683

  19. Isolation and characterization of microsatellite markers in the Lepisorus clathratus complex (Polypodiaceae)1

    PubMed Central

    Zhao, Cun-Feng; Kwak, Myounghai; Xiang, Qiao-Ping

    2016-01-01

    Premise of the study: Microsatellites were designed and characterized in the Sino-Himalayan fern Lepisorus clathratus complex (Polypodiaceae) to further study the phylogeography and reproductive ecology of this species. Methods and Results: From a genomic library obtained by next-generation sequencing, 10 polymorphic and six monomorphic microsatellite loci were developed. In one population of L. clathratus from Taibaishan in central China, the number of alleles observed for these microsatellites ranged from seven to 29, and observed and expected heterozygosity ranged from 0.463 to 0.919 and from 0.797 to 0.947, respectively. Cross-amplification in other taxa within this complex was successful, but cross-amplification was poor for other congeneric species. Conclusions: This set of newly developed microsatellite markers will be useful for assessing genetic diversity, population structure, and mating system, and to infer polyploid origin in the L. clathratus complex. PMID:27785385

  20. Genetic variation at microsatellite loci in the tropical herb Aphelandra aurantiaca (Acanthaceae)1

    PubMed Central

    Suárez-Montes, Pilar; Tapia-López, Rosalinda; Núñez-Farfán, Juan

    2015-01-01

    Premise of the study: To assess the effect of forest fragmentation on genetic variation and population structure of Aphelandra aurantiaca (Acanthaceae), a tropical and ornamental herbaceous perennial plant, we developed the first microsatellite primers for the species. Methods and Results: Fourteen microsatellite markers were isolated and characterized from A. aurantiaca genomic libraries enriched for di-, tri-, and tetranucleotide repeat motifs. Polymorphism was evaluated in 107 individuals from four natural populations. Twelve out of 14 genetic markers were polymorphic. The number of alleles per locus ranged from two to 12, and the observed and expected heterozygosities ranged from 0.22 to 0.96 and from 0.20 to 0.87, respectively. Fixation indices ranged from −0.41 to 0.44. Conclusions: These newly developed microsatellite markers for A. aurantiaca will be useful for future population genetic studies, specifically to detect the possible loss of genetic diversity due to habitat fragmentation. PMID:26649265

  1. Characterization of 13 microsatellite markers for Diuris basaltica (Orchidaceae) and related species1

    PubMed Central

    Ahrens, Collin W.; James, Elizabeth A.

    2014-01-01

    • Premise of the study: Diuris basaltica (Orchidaceae) is an endangered forb on the Victorian grasslands and has many close relatives. Microsatellite markers have been developed to facilitate assessment of population structure within D. basaltica and among related taxa within the species complex. • Methods and Results: Twenty-five microsatellite markers (13 polymorphic and 12 monomorphic) were developed from D. basaltica using 454 pyrosequencing, and all primer pairs were amplified in D. gregaria and D. chryseopsis. For the set of polymorphic markers, the number of alleles per locus ranged from one to 10, two to nine, and two to 18 for D. basaltica, D. gregaria, and D. chryseopsis, respectively. The expected and observed heterozygosities ranged from 0.18 to 0.95 and 0.14 to 0.86, respectively. • Conclusions: The microsatellite markers developed in this study can be used to analyze the population genetic structure of D. basaltica and other Diuris species. PMID:25202591

  2. Isolation and characterization of 12 microsatellite loci in soapbark, Quillaja saponaria (Quillajaceae)1

    PubMed Central

    Letelier, Luis; Harvey, Nick; Valderrama, Aly; Stoll, Alexandra; González-Rodríguez, Antonio

    2015-01-01

    Premise of the study: Microsatellite primers were developed for the endemic Chilean tree Quillaja saponaria (Quillajaceae), a common member of the sclerophyllous Mediterranean forest, to investigate intraspecific patterns of genetic diversity and structure. Methods and Results: Using an enriched library, 12 polymorphic microsatellite loci were developed in Q. saponaria. All loci consisted of dinucleotide repeats. The average number of alleles per locus was 5.3 (2–13), with a total of 64 alleles recorded in 39 individuals from three populations. Conclusions: The microsatellite markers described here are the first characterized for Q. saponaria. The polymorphic loci will be useful in studies of genetic diversity and genetic population differentiation in natural populations of this species. PMID:25995980

  3. Characterization of nuclear microsatellite markers for Rumex bucephalophorus (Polygonaceae) using 454 sequencing1

    PubMed Central

    Viruel, Juan; Ortiz, Pedro L.; Arista, Montserrat; Talavera, María

    2015-01-01

    Premise of the study: Nuclear microsatellite markers were developed in Rumex bucephalophorus subsp. canariensis (Polygonaceae) to investigate its genetic diversity and structure. Methods and Results: Sixteen polymorphic microsatellite markers were obtained using 454 next-generation sequencing with di-, tri-, and tetranucleotide repeats. The average number of alleles was 5.688 and 3.813 for R. bucephalophorus subsp. canariensis var. canariensis and var. fruticescens, respectively. Slightly higher levels of mean genetic diversity were found in var. canariensis (expected heterozygosity = 0.600) than in var. fruticescens (expected heterozygosity = 0.514). Cross-amplifications in related taxa within R. bucephalophorus showed good amplification and polymorphic patterns. Conclusions: These 16 novel nuclear microsatellite markers are the first in the genus Rumex and may serve as valuable tools to carry out studies on genetic diversity and structure as well as progeny studies. PMID:26697279

  4. Whole genome shotgun sequences for microsatellite discovery and application in cultivated and wild Macadamia (Proteaceae)1

    PubMed Central

    Nock, Catherine J.; Elphinstone, Martin S.; Ablett, Gary; Kawamata, Asuka; Hancock, Wayne; Hardner, Craig M.; King, Graham J.

    2014-01-01

    • Premise of the study: Next-generation sequencing (NGS) data are widely used for single-nucleotide polymorphism discovery and genetic marker development in species with limited available genome information. We developed microsatellite primers for the Proteaceae nut crop species Macadamia integrifolia and assessed cross-species transferability in all congeners to investigate genetic identification of cultivars and gene flow. • Methods and Results: Primers were designed from both raw and assembled Illumina NGS paired-end reads. The final 12 microsatellite markers selected were polymorphic among wild individuals of all four Macadamia species—M. integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii—and in commercial macadamia cultivars including hybrids. • Conclusions: We demonstrate the utility of raw and assembled Illumina NGS reads from total genomic DNA for the rapid development of microsatellites in Macadamia. These primers will facilitate future studies of population structure, hybridization, parentage, and cultivar identification in cultivated and wild Macadamia populations. PMID:25202615

  5. Development of microsatellite markers using Illumina MiSeq sequencing to characterize Ephedra gerardiana (Ephedraceae)1

    PubMed Central

    De, Ji; Zhu, Weidong; Liu, Tianmeng; Wang, Zhe; Zhong, Yang

    2017-01-01

    Premise of the study: Ephedra gerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. Methods and Results: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E. gerardiana, of which 15 loci also showed polymorphisms in two related Ephedra species, E. saxatilis and E. monosperma. The average number of effective alleles per locus ranged from two to six. The observed and expected heterozygosity ranged from 0.23 to 0.83 and 0.44 to 0.86, respectively, in E. gerardiana populations. Conclusions: The developed 29 microsatellite markers are effective for the study of genetic structure and genetic diversity of E. gerardiana, and 15 of these markers are suitable for related Ephedra species. PMID:28337389

  6. Development and characterization of nine microsatellites for an endangered tree, Pinus wangii (Pinaceae)1

    PubMed Central

    Dou, Jing-Jing; Zhou, Ren-Chao; Tang, An-Jun; Ge, Xue-Jun; Wu, Wei

    2013-01-01

    • Premise of the study: Pinus wangii is an endemic and endangered species in southwestern China, and microsatellite primers were developed to characterize its genetic diversity and population structure. • Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, nine sets of microsatellite primers were developed in P. wangii. One population with 26 individuals of P. wangii, as well as 11 individuals each for two congeneric species, P. taiwanensis and P. squamata, were used to test their polymorphism and transferability. The number of alleles per locus ranged from one to seven with an average of 3.7, and the observed heterozygosity and expected heterozygosity ranged from 0 to 0.91 and 0 to 0.75, respectively. • Conclusions: We developed nine sets of polymorphic microsatellite loci that are suitable for investigating genetic diversity and population structure of P. wangii, and these markers may be useful for other Pinus species. PMID:25202511

  7. Isolation and characterization of microsatellite loci from the soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ten novel microsatellite loci were isolated and characterized from the soybean aphid, APHIS GLYCINES, a serious invasive pest of soybeans in North America. The isolated loci were polymorphic, with two to 19 alleles in 48 wild individuals collected from Korea, Japan, and the United States. All loci ...

  8. Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 1...

  9. Isolation and characterization of 108 novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus)

    EPA Science Inventory

    We characterized 108 polymorphic microsatellite loci for the mummichog (Fundulus heteroclitus), an Atlantic coastal killifish. Allelic diversity among 26 individuals ranged between 2 and 15 alleles per locus, while expected heterozygosity ranged from 0.075 to 0.904. Significant ...

  10. Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international demands fro...

  11. De novo genome assembly of Cercospora beticola for microsatellite marker development and validation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cercospora leaf spot caused by Cercospora beticola is a significant threat to the production of sugar and table beet worldwide. A de novo genome assembly of C. beticola was used to develop eight polymorphic and reproducible microsatellite markers for population genetic analyses. These markers were u...

  12. Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Eight microsatellite DNA markers were developed for studies of gene flow in the redbud tree (Cercis canadensis), which is native to North America. The loci were unlinked and polymorphic in a sample of 22 individuals collected from a single population in Oak Ridge, Tennessee. Allele number ranged fr...

  13. Isolation and characterization of microsatellite loci from the yellow-eyed penguin (Megadyptes antipodes).

    PubMed

    Boessenkool, S; King, T M; Seddon, P J; Waters, J M

    2008-09-01

    Twelve microsatellite loci were isolated and characterized in the endangered yellow-eyed penguin (Megadyptes antipodes) using enriched genomic libraries. Polymorphic loci revealed two to eight alleles per locus and observed heterozygosity ranged from 0.21 to 0.77. These loci will be suitable for assessing current and historical patterns of genetic variability in yellow-eyed penguins.

  14. Development and characterization of microsatellites for switchgrass rust fungus (Puccinia emaculata)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ten polymorphic microsatellite loci from the fungus Puccinia emaculata, responsible for rust disease of switchgrass (Panicum virgatum) were developed. Loci were characterized using 20 single-pustule derived isolates of P. emaculata collected from switchgrass plants growing in the southeastern US. Th...

  15. Eight microsatellite loci in Phaedranassa schizantha Baker (Amaryllidaceae) and cross-amplification in other Phaedranassa species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phaedranassa schizantha is a species endemic to Ecuador from which eight polymorphic microsatellite loci were isolated from an enriched genomic library. A total of 31 alleles with an average of four alleles per locus were detected across 29 individuals from a single natural population of P. schizan...

  16. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications.

    PubMed

    Queirós, J; Godinho, R; Lopes, S; Gortazar, C; de la Fuente, J; Alves, P C

    2015-07-01

    Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.

  17. [Screening of peafowl microsatellite primers and analysis of genetic diversity].

    PubMed

    Bao, Wen-Bin; Chen, Guo-Hong; Shu, Jing-Ting; Xu, Qi; Li, Hui-Fang

    2006-10-01

    The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing.

  18. Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences.

    PubMed

    Liu, Xinlong; Li, Xujuan; Liu, Hongbo; Xu, Chaohua; Lin, Xiuqin; Li, Chunjia; Deng, Zuhu

    2016-01-01

    Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy clones have been utilized successfully in improving the stress resistance and yield related traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evolutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA-ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and analyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor selected as controls. The results showed that decaploid clones (2n = 80) possess the most abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid and decaploid populations. By comparing the genetic distances among four ploidy populations, the dodecaploid population exhibited the closest relationship with the nonaploid population, and then the relationship strength decreased successively for the decaploid population and then for the octaploid population. Population differentiation analysis showed that the phenomena of population differentiation were not found among different ploidy populations, and low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these populations possessing close genetic relationship. These results mentioned above will contribute to the understanding of the evolution of different ploidy populations of Saccharum spontaneum and provide vital knowledge for their utilization in sugarcane breeding and innovation.

  19. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys

    PubMed Central

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-01

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

  20. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.

    PubMed

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-26

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species.

  1. Does the evolutionary conservation of microsatellite loci imply function?

    SciTech Connect

    Shriver, M.D.; Deka, R.; Ferrell, R.E.

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  2. Microsatellite and trinucleotide-repeat evolution: evidence for mutational bias and different rates of evolution in different lineages.

    PubMed Central

    Rubinsztein, D C; Amos, B; Cooper, G

    1999-01-01

    Microsatellites are stretches of repetitive DNA, where individual repeat units comprise one to six bases. These sequences are often highly polymorphic with respect to repeat number and include trinucleotide repeats, which are abnormally expanded in a number of diseases. It has been widely assumed that microsatellite loci are as likely to gain and lose repeats when they mutate. In this review, we present population genetic and empirical data arguing that microsatellites, including normal alleles at trinucleotide-repeat disease loci, are more likely to expand in length when they mutate. In addition, our experiments suggest that the rates of expansion of such sequences differ in related species. PMID:10434312

  3. Determination of Phylogenetic and Molecular Characteristics of Three Malaysian Ginger Cultivars (Zingiber officinale Roscoe) Using Microsatellite DNA

    PubMed Central

    Mahdi, Harith Jameel; Andayani, Retno; Aziz, Ishak

    2013-01-01

    Three Malaysian ginger cultivars (Bukit Tinggi, Tanjung Sepat and Sabah) were collected and examined for genetic polymorphisms using microsatellite DNA primers. The single microsatellite oligonucleotide primers (CATA)5, (GATA)5 and (GAC)6 were used in polymerase chain reactions (PCRs). These PCR reactions produced 7 polymorphic bands with an average of 2.334 polymorphic bands per primer, leading to an average polymorphism rate of 17.9%. Cluster analysis revealed 87.50% similarity between Bukit Tinggi and Tanjung Sepat, 64.27% similarity between Bukit Tinggi and Sabah and 56.25% similarity between Tanjung Sepat and Sabah. DNA sequencing of the polymorphic PCR products of Tanjung Sepat ginger revealed the characteristic features of a putative new gene: a core promoter sequence, an enhancer and a transcription start site. Cluster analysis using the unweighted pair group method with arithmetic average (UPGMA) was used to construct a phylogenetic tree, which indicated that Bukit Tinggi ginger is genetically more closely related to Tanjung Sepat ginger than to Sabah ginger. Based on the results of this study, we concluded that there is genotypic variation among ginger cultivars, and the microsatellite DNA primers described here are useful for detecting polymorphic DNA in Malaysian ginger cultivars. Additionally, these microsatellite DNA primers may be used as molecular markers for discriminating among select Malaysian ginger cultivars. PMID:24575249

  4. Determination of Phylogenetic and Molecular Characteristics of Three Malaysian Ginger Cultivars (Zingiber officinale Roscoe) Using Microsatellite DNA.

    PubMed

    Mahdi, Harith Jameel; Andayani, Retno; Aziz, Ishak

    2013-12-01

    Three Malaysian ginger cultivars (Bukit Tinggi, Tanjung Sepat and Sabah) were collected and examined for genetic polymorphisms using microsatellite DNA primers. The single microsatellite oligonucleotide primers (CATA)5, (GATA)5 and (GAC)6 were used in polymerase chain reactions (PCRs). These PCR reactions produced 7 polymorphic bands with an average of 2.334 polymorphic bands per primer, leading to an average polymorphism rate of 17.9%. Cluster analysis revealed 87.50% similarity between Bukit Tinggi and Tanjung Sepat, 64.27% similarity between Bukit Tinggi and Sabah and 56.25% similarity between Tanjung Sepat and Sabah. DNA sequencing of the polymorphic PCR products of Tanjung Sepat ginger revealed the characteristic features of a putative new gene: a core promoter sequence, an enhancer and a transcription start site. Cluster analysis using the unweighted pair group method with arithmetic average (UPGMA) was used to construct a phylogenetic tree, which indicated that Bukit Tinggi ginger is genetically more closely related to Tanjung Sepat ginger than to Sabah ginger. Based on the results of this study, we concluded that there is genotypic variation among ginger cultivars, and the microsatellite DNA primers described here are useful for detecting polymorphic DNA in Malaysian ginger cultivars. Additionally, these microsatellite DNA primers may be used as molecular markers for discriminating among select Malaysian ginger cultivars.

  5. Functional interaction between SNPs and microsatellite in the transcriptional regulation of insulin-like growth factor 1.

    PubMed

    Chen, Holly Y; Huang, Wei; Leung, Vincent H K; Fung, Simon L M; Ma, Suk Ling; Jiang, Hongling; Tang, Nelson L S

    2013-09-01

    A CA-repeat microsatellite in insulin-like growth factor 1 (IGF1) promoter was associated with interindividual variation of circulating IGF1 level. Previously, we reported that such association was due to variation of haplotype unit in a linkage disequilibrium block composed of microsatellite and single-nucleotide polymorphisms (SNPs), suggesting the presence of an interaction between them. In this study, reporter assays were performed to investigate the regulatory effect and interaction of genetic variants on gene expression. We used an in vitro system to compare the transcriptional activities of haplotypes (rs35767:T>C, the CA-repeat microsatellite, rs5742612:T>C, and rs2288377:T>A) in evolutionarily conserved region of IGF1 promoter. In haplotype C-T-T, a longer microsatellite had a lower transcriptional activity (17.6 ± 2.4-fold for 17 repeats and 8.3 ± 1.1-fold for 21 repeats), whereas in haplotype T-C-A, such trend could not be observed, as the microsatellite with 21 repeats had the highest transcriptional activity (17.5 ± 2.3-fold). Because the microsatellite and SNPs affected the transcriptional activity of each other, there may be an interaction between them in the regulation of IGF1 expression. For the first time, we demonstrated that a noncoding microsatellite polymorphism could act as a functional unit and interact with SNPs in the regulation of transcription in human genome.

  6. Rapid Microsatellite Isolation from a Butterfly by De Novo Transcriptome Sequencing: Performance and a Comparison with AFLP-Derived Distances

    PubMed Central

    Mikheyev, Alexander S.; Vo, Tanya; Wee, Brian; Singer, Michael C.; Parmesan, Camille

    2010-01-01

    Background The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). Principal Findings By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations). Significance De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes. PMID:20585453

  7. Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites.

    PubMed

    Sudheer, Pamidimarri D V N; Rahman, Hifzur; Mastan, Shaik G; Reddy, Muppala P

    2010-12-01

    Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J

  8. Comparative analysis of intermuscular bones in fish of different ploidies.

    PubMed

    Li, Ling; Zhong, Zezhou; Zeng, Ming; Liu, Shaojun; Zhou, Yi; Xiao, Jun; Wang, Jun; Liu, Yun

    2013-04-01

    We documented the number, morphology, and distribution of intermuscular bones in five fishes of different ploidy: Carassius auratus (Abbr.WCC, 2n=100), Carassius auratus variety PengZe (Abbr.PZCC, 3n=150), improved triploid crucian carp (Abbr.ITCC, 3n=150), improved red crucian carp (Carassius auratus red var., Abbr.IRCC, ♀, 2n=100), and improved allotetraploids (Abbr.G×AT, ♂, 4n=200). The number of intermuscular bones in WCC, PZCC, and G×AT ranged from 78 to 83 ([Formula: see text]=81), 80 to 86 ([Formula: see text]=84), and 77 to 84 ([Formula: see text]=82), respectively. The numbers in ITCC and IRCC were significantly lower, ranging from 77 to 82 ([Formula: see text]=79) and 58 to 77 ([Formula: see text]=71), respectively. The average number of intermuscular bones in each sarcomere, ranked in order from highest to lowest, was 0.721 (WCC), 0.673 (PZCC), 0.653 (G×AT), 0.633 (ITCC), and 0.608 (IRCC). There was no difference between ITCC and G×AT or between G×AT and PZCC. However, the average number of intermuscular bones in the sarcomeres of ITCC, WCC, and PZCC differed significantly, as did that of IRCC and the four other kinds of fish. The intermuscular bone of these five fishes was divided into seven shape categories, non-forked (), one-end-unequal-bi-fork (), one-end-equal-bi-fork (Y), one-end-multi-fork, two-end-bi-fork, two-end-multi-fork, and tree-branch types. Generally, the morphological complexity was higher in the anterior intermuscular bones than in the posterior body. The number of intermuscular bones was similar but not equal between the left and right sides of the body. ITCC had significantly fewer intermuscular bones than either WCC or PZCC, making it of greater commercial value. Additionally, IRCC and ITCC had fewer intermuscular bones than WCC. Our observations are significant in both fish bone developmental biology and genetic breeding.

  9. [Analysis of the level and pattern of genomic DNA methylation in different ploidy watermelons by MSAP (Citrullus lanatus)].

    PubMed

    Wang, Chun Guo; Gu, Yu; Chen, Cheng Bin; Jiao, Ding Liang; Xue, Zhen Yi; Song, Wen Qin

    2009-04-01

    DNA methylation is one of the major epigenetic modifications. It is very important to the regulation of gene expression. In present study, an autoploidy series (2x, 3x and 4x) in watermelon (Citrullus lanatus) was constructed and MSAP (Methylation-Sensitive Amplification Polymorphism) analysis was conducted to elucidate the level and pattern of DNA methylation at CCGG sites in different ploidy watermelons. Totally, 1883 genetic loci were produced by 23 pairs of selective primers, of which 647, 655 and 581 sites were detected in diploid, autotriploid and autotetraploid, respectively. The methylation sites were 181, 150 and 159, and the corresponding total methylation ratios were 28.0%, 22.9% and 27.4% in 2x, 3x and 4x, respectively, of which the fully methylation sites were 121, 80 and 82, and the corresponding fully methylation ratios were 18.7%, 12.2% and 14.1%. Further analysis of the pattern of DNA methylation suggested that compared 4x with 2x, about half of detected sites (54.4%) shown changes of DNA methylation patterns. Similarly, compared 4x with 3x, 45.4% sites also shown changes of DNA methylation patterns. Moreover, the trend of DNA methylation adjustment mainly involved increase of DNA methylation levels in 4x. However, compared 3x with 2x or 4x, although the changes of DNA methylation pattern also widely occurred, which involved 41.6% (compared 3x with 2x) and 45.4% (compared 3x with 4x) sites, respectively, the trend of DNA methylation adjustment mainly involved decrease of DNA methylation levels in 3x. All these results indicated that DNA methylation events were widely existed in different ploidy watermelons. However, not only based on the total DNA methylation ratio or fully DNA methylation ratio, the results both implied that the DNA methylation levels were not closely associated with the autopolyploidy level in watermelon. Autotriploid watermelon shows obvious low level of DNA methylation. Analysis of DNA methylation patterns also suggested that

  10. Development and characterization of 27 microsatellite markers for the mangrove fern, Acrostichum aureum (Pteridaceae)1

    PubMed Central

    Yamamoto, Takashi; Tsuda, Yoshiaki; Mori, Gustavo Maruyama; Cruz, Mariana Vargas; Shinmura, Yoshimi; Wee, Alison K. S.; Takayama, Koji; Asakawa, Takeshi; Yamakawa, Takeru; Suleiman, Monica; Núñez-Farfán, Juan; Webb, Edward L.; Watano, Yasuyuki; Kajita, Tadashi

    2016-01-01

    Premise of the study: Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant. Methods and Results: Fifty-six A. aureum individuals from three populations were sampled and genotyped to characterize the 27 loci. The number of alleles and expected heterozygosity ranged from one to 15 and 0.000 to 0.893, respectively. Across the 26 polymorphic loci, the Malaysian population showed much higher levels of polymorphism compared to the other two populations in Guam and Brazil. Cross-amplification tests in the other two species from the genus determined that seven and six loci were amplifiable in A. danaeifolium and A. speciosum, respectively. Conclusions: The 26 polymorphic microsatellite markers will be useful for future studies investigating the genetic structure and demographic history of of A. aureum, which has the widest distributional range of all mangrove plants. PMID:27672519

  11. Development of microsatellite markers for the apomictic triploid fern Myriopteris lindheimeri (Pteridaceae)1

    PubMed Central

    Grusz, Amanda L.; Pryer, Kathleen M.

    2015-01-01

    Premise of the study: Microsatellite markers were developed for investigating the population dynamics of Myriopteris lindheimeri (Pteridaceae), an apomictic triploid fern endemic to deserts of the southwestern United States and Mexico. Methods and Results: Using 454 sequencing, 21 microsatellite markers were developed. Of these, 14 were polymorphic with up to five alleles per locus and eight markers amplified in one or more congeneric close relatives (M. covillei, M. fendleri, M. aurea, and M. rufa). To demonstrate marker utility, M. lindheimeri samples from three Arizona populations were genotyped at nine loci. For each population, diversity measures including percent polymorphic loci, frequency of heterozygotes across all loci, and genotypic diversity were calculated. Across the three populations, on average, 63% of loci were polymorphic, the average frequency of heterozygotes (across all loci) was 0.32, and average genotypic diversity was 0.34. Conclusions: These markers provide a foundation for future studies exploring polyploidy and apomixis in myriopterid ferns. PMID:26649266

  12. Microsatellite markers for Nuphar japonica (Nymphaeaceae), an aquatic plant in the agricultural ecosystem of Japan1

    PubMed Central

    Kondo, Toshiaki; Watanabe, Sonoko; Shiga, Takashi; Isagi, Yuji

    2016-01-01

    Premise of the study: Nuphar species (Nymphaeaceae) are representative aquatic plants in irrigation ponds in Japanese agricultural ecosystems. We developed 15 polymorphic microsatellite markers for N. japonica and confirmed their utility for its close relatives N. oguraensis var. akiensis and N. ×saijoensis, which originated from natural hybridization between N. japonica and N. oguraensis. Methods and Results: Genetic variation was characterized in 15 polymorphic loci in three populations of N. japonica. The average number of alleles per locus was 3.47 (range = 2−9; n = 32), and the average expected heterozygosity per locus was 0.84 (range = 0.5–1.0); 11 loci were amplified in N. oguraensis var. akiensis and 15 in N. ×saijoensis. Conclusions: The polymorphic microsatellite markers developed in this study will be useful for investigating the levels of genetic diversity within remnant populations of Nuphar taxa and could provide a valuable tool for conservation genetics of these taxa. PMID:28101435

  13. Development and characterization of 15 microsatellite markers for Cephalotaxus fortunei (Cephalotaxaceae)1

    PubMed Central

    Wang, Chunbo; Guo, Zhiyou; Huang, Xilian; Huang, Lu

    2016-01-01

    Premise of the study: To survey population variation and the adaptive evolution of Cephalotaxus fortunei (Cephalotaxaceae), an endemic and endangered conifer in China, microsatellite markers were developed and characterized for this species. Methods and Results: Based on the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 15 microsatellite markers were developed for C. fortunei, 13 of which were polymorphic within a sample of 75 individuals representing five natural populations. The number of alleles per locus ranged from one to seven. The expected and observed heterozygosities were 0.108–0.738 and 0.000–1.000, respectively. Ten polymorphic loci were also successfully amplified in C. oliveri. Conclusions: These polymorphic loci provide a valuable tool for population genetic analysis of C. fortunei, which will contribute to its management and conservation. PMID:27213121

  14. Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae)1

    PubMed Central

    Klabunde, Gustavo H. F.; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I.; Nodari, Rubens O.

    2014-01-01

    • Premise of the study: Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • Methods and Results: A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)–enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • Conclusions: These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana. PMID:25202632

  15. Isolation and characterization of novel microsatellites for Abies koreana and A. nephrolepis (Pinaceae).

    PubMed

    Hong, J K; Lim, J; Lee, B Y; Kwak, M

    2016-04-28

    Abies koreana is an endemic and rare species from Korea and is classified as endangered by the International Union for Conservation of Nature. Although the genetic diversity assessment for current population of A. koreana needs to be performed urgently, no microsatellite markers have been developed for this species. In the present study, we developed 22 novel polymorphic microsatellite loci and the characteristics of these loci were determined in A. koreana as well as in Abies nephrolepis, the most closely related species, and these loci were compared with previously reported microsatellite markers developed for the Abies genus. Genomic sequence (161 Mbp; 325,776 reads) was obtained from one individual of A. koreana using Roche 454 GS-FLX Titanium sequencing and 19,258 repeat motifs were identified from it. A total of 288 primer pairs with high copy numbers of di-repeat motifs were evaluated for amplification in A. koreana and A. nephrolepis. A total of 71 primer pairs successfully amplified fragments, of which 22 showed polymorphisms in A. koreana and A. nephrolepis. The average expected diversity was 0.767 and 0.717 in A. koreana and A. nephrolepis, respectively; these heterozygosity levels were moderate compared to the previously reported microsatellite loci from Abies species. This is the first set of microsatellite markers developed for A. koreana as well as A. nephrolepis and further population genetic studies of both species and genetic delimitation can be carried out for the species conservation and management.

  16. Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci.

    PubMed

    Bulut, Zafer; McCormick, Cory R; Gopurenko, David; Williams, Rod N; Bos, David H; DeWoody, J Andrew

    2009-07-01

    Microsatellites are commonly used for mapping and population genetics because of their high heterozygosities and allelic variability (i.e., polymorphism). Microsatellite markers are generally more polymorphic than other types of molecular markers such as allozymes or SNPs because the insertions/deletions that give rise to microsatellite variability are relatively common compared to nucleotide substitutions. Nevertheless, direct evidence of microsatellite mutation rates (MMRs) is lacking in most vertebrate groups despite the importance of such estimates to key population parameters (e.g., genetic differentiation or theta = 4N (e)micro). Herein, we present empirical data on MMRs in eastern tiger salamanders (Ambystoma tigrinum tigrinum). We conducted captive breeding trials and genotyped over 1,000 offspring at a suite of microsatellite loci. These data on 7,906 allele transfers provide the first direct estimates of MMRs in amphibians, and they illustrate that MMRs can vary by more than an order of magnitude across loci within a given species (one locus had ten mutations whereas the others had none).

  17. Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis

    PubMed Central

    Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

    2016-01-01

    Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy–Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies. PMID:27197749

  18. Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

    PubMed

    Lee, Gi-An; Song, Jae Young; Choi, Heh-Ran; Chung, Jong-Wook; Jeon, Young-Ah; Lee, Jung-Ro; Ma, Kyung-Ho; Lee, Myung-Chul

    2015-04-10

    The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  19. Isolation and characterization of microsatellite loci in the Chinese Cobra Naja atra (Elapidae).

    PubMed

    Lin, Long-Hui; Mao, Lu-Xi; Luo, Xia; Qu, Yan-Fu; Ji, Xiang

    2011-01-01

    We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.

  20. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome.

    PubMed

    Menotti-Raymond, M; David, V A; Agarwala, R; Schäffer, A A; Stephens, R; O'Brien, S J; Murphy, W J

    2003-01-01

    Effective utilization of the domestic cat as an animal model for hereditary and infectious disease requires the development and implementation of high quality gene maps incorporating microsatellites and conserved coding gene markers. Previous feline linkage and radiation hybrid maps have lacked sufficient microsatellite coverage on all chromosomes to make effective use of full genome scans. Here we report the isolation and genomic mapping of 304 novel polymorphic repeat loci in the feline genome. The new loci were mapped in the domestic cat radiation hybrid panel using an automated fluorescent TAQ-Man based assay. The addition of these 304 microsatellites brings the total number of microsatellites mapped in the feline genome to 580, and the total number of loci placed onto the RH map to 1,126. Microsatellites now span every autosome with an average spacing of roughly one polymorphic STR every five centimorgans, and full genome coverage of one marker every 2.7 megabases. These loci now provide a useful tool for undertaking full-genome scans to identify genes associated with phenotypes of interest, such as those relating to hereditary disease, coat color, patterning and morphology. These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses.

  1. Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin.

    PubMed

    Jungmann, L; Vigna, B B Z; Boldrini, K R; Sousa, A C B; do Valle, C B; Resende, R M S; Pagliarini, M S; Zucchi, M I; de Souza, A P

    2010-09-01

    Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.

  2. Three-dimensional direct measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections

    NASA Astrophysics Data System (ADS)

    Bensley, Jonathan Guy; de Matteo, Robert; Harding, Richard; Black, Mary Jane

    2016-04-01

    Quantitative assessment of myocardial development and disease requires accurate measurement of cardiomyocyte volume, nuclearity (nuclei per cell), and ploidy (genome copies per cell). Current methods require enzymatically isolating cells, which excludes the use of archived tissue, or serial sectioning. We describe a method of analysis that permits the direct simultaneous measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections. To demonstrate the utility of our technique, heart tissue was obtained from four species (rat, mouse, rabbit, sheep) at up to three life stages: prenatal, weaning and adulthood. Thick (40 μm) paraffin sections were stained with Wheat Germ Agglutinin-Alexa Fluor 488 to visualise cell membranes, and DAPI (4‧,6-diamidino-2-phenylindole) to visualise nuclei and measure ploidy. Previous methods have been restricted to thin sections (2–10 μm) and offer an incomplete picture of cardiomyocytes. Using confocal microscopy and three-dimensional image analysis software (Imaris Version 8.2, Bitplane AG, Switzerland), cardiomyocyte volume, nuclearity, and ploidy were measured. This method of staining and analysis of cardiomyocytes enables accurate morphometric measurements in thick histological sections, thus unlocking the potential of archived tissue. Our novel time-efficient method permits the entire cardiomyocyte to be visualised directly in 3D, eliminating the need for precise alignment of serial sections.

  3. Three-dimensional direct measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections

    PubMed Central

    Bensley, Jonathan Guy; De Matteo, Robert; Harding, Richard; Black, Mary Jane

    2016-01-01

    Quantitative assessment of myocardial development and disease requires accurate measurement of cardiomyocyte volume, nuclearity (nuclei per cell), and ploidy (genome copies per cell). Current methods require enzymatically isolating cells, which excludes the use of archived tissue, or serial sectioning. We describe a method of analysis that permits the direct simultaneous measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections. To demonstrate the utility of our technique, heart tissue was obtained from four species (rat, mouse, rabbit, sheep) at up to three life stages: prenatal, weaning and adulthood. Thick (40 μm) paraffin sections were stained with Wheat Germ Agglutinin-Alexa Fluor 488 to visualise cell membranes, and DAPI (4′,6-diamidino-2-phenylindole) to visualise nuclei and measure ploidy. Previous methods have been restricted to thin sections (2–10 μm) and offer an incomplete picture of cardiomyocytes. Using confocal microscopy and three-dimensional image analysis software (Imaris Version 8.2, Bitplane AG, Switzerland), cardiomyocyte volume, nuclearity, and ploidy were measured. This method of staining and analysis of cardiomyocytes enables accurate morphometric measurements in thick histological sections, thus unlocking the potential of archived tissue. Our novel time-efficient method permits the entire cardiomyocyte to be visualised directly in 3D, eliminating the need for precise alignment of serial sections. PMID:27048757

  4. Genetic diversity and differentiation in Camellia reticulata (Theaceae) polyploid complex revealed by ISSR and ploidy.

    PubMed

    Wang, B-Y; Ruan, Z-Y

    2012-03-06

    Camellia reticulata is a well-known ornamental and oil plant that is endemic to southwest China. This species shows three cell ploidies, i.e., diploidy, tetraploidy and hexaploidy. We made the first investigation of genetic diversity and differentiation of natural populations of C. reticulata, and 114 individuals from 6 populations were sampled. Cytogeography results showed that ploidy is invariable within populations and evenly distributed. A relatively high level of genetic diversity was found in C. reticulata, both at the species level (PPB = 88.89%; H = 0.2809; I = 0.4278) and at the population level (mean PPB = 42.13%; mean H = 0.14; mean I = 0.21). We found a relatively low degree of differentiation among ploidies (G(ST) = 0.2384; AMOVA = 10.26%) and a relatively high degree of differentiation among populations (G(CS) = 0.3807; AMOVA = 48.75%). The high genetic diversity can be explained by its biological character, wide distribution and ploidies, and the special genetic structure can be ascribed to polyploid origin from hybridization with different Camellia spp. This information will be useful for the introduction, conservation and further studies of C. reticulata and related species.

  5. Diploid-triploid mosaicism and tissue ploidy diversity within Platemys platycephala from Suriname.

    PubMed

    Bickham, J W; Hanks, B G

    2009-01-01

    The twist-necked turtle, Platemys platycephala, is 1 of only 2 known species to possess sexual reproduction and diploid-triploid mosaicism. Previous studies have shown that mosaics occur in Suriname and French Guiana but only diploids are known from Bolivia and Brazil. In this paper, the frequency of ploidy mosaicism was studied in a large sample of P. platycephala from Suriname to more fully explore the diversity of ploidy levels within and among individuals. Flow-cytometric analysis of blood revealed a wide diversity of conditions including diploids, diploid-triploid mosaics, triploids, and triploid-tetraploid mosaics. The largest frequency class was 100% diploid, and the second largest was 100% triploid. However, mosaic individuals were observed from the entire spectrum of mixtures ranging from nearly all-diploid to nearly all-triploid and 2 individuals were triploid-tetraploid mosaics. It appears likely that diploids, triploids and mosaics do not represent distinct biotypes, but simply different conditions within a spectrum of possible ploidy mixtures. Studies of multiple tissues from 5 individuals showed blood alone is a good indicator of ploidy, but subtle differences were found among tissues for some individuals, and some individuals that were all-diploid or all-triploid in blood were found to be mosaic in other tissues. Triploidy was statistically associated with males, and we hypothesize that genome size plays a role in sex determination in this species.

  6. The ploidy conveyor of mature hepatocytes as a source of genetic variation.

    PubMed

    Duncan, Andrew W; Taylor, Matthew H; Hickey, Raymond D; Hanlon Newell, Amy E; Lenzi, Michelle L; Olson, Susan B; Finegold, Milton J; Grompe, Markus

    2010-10-07

    Mononucleated and binucleated polyploid hepatocytes (4n, 8n, 16n and higher) are found in all mammalian species, but the functional significance of this conserved phenomenon remains unknown. Polyploidization occurs through failed cytokinesis, begins at weaning in rodents and increases with age. Previously, we demonstrated that the opposite event, ploidy reversal, also occurs in polyploid hepatocytes generated by artificial cell fusion. This raised the possibility that somatic 'reductive mitoses' can also happen in normal hepatocytes. Here we show that multipolar mitotic spindles form frequently in mouse polyploid hepatocytes and can result in one-step ploidy reversal to generate offspring with halved chromosome content. Proliferating hepatocytes produce a highly diverse population of daughter cells with multiple numerical chromosome imbalances as well as uniparental origins. Our findings support a dynamic model of hepatocyte polyploidization, ploidy reversal and aneuploidy, a phenomenon that we term the 'ploidy conveyor'. We propose that this mechanism evolved to generate genetic diversity and permits adaptation of hepatocytes to xenobiotic or nutritional injury.

  7. Isolation and characterization of microsatellite markers for the tree-root endophytes Phialocephala subalpina and Phialocephala fortinii s.s.

    PubMed

    Queloz, Valentin; Duò, Angelo; Grünig, Christoph R

    2008-11-01

    Species of the Phialocephala fortinii s.l.-Acephala applanata complex are the dominant dark septate endophytes (DSE) in roots of species belonging to the Pinaceae. The two species Phialocephala subalpina and P. fortinii s.s. belong to the most widely distributed species within this complex. In the present study, 15 polymorphic microsatellite loci were developed for these two closely related species. Strains of a community which were analysed previously using single-copy restriction fragment length polymorphism were screened with the new markers. Microsatellites were suitable to classify the two species and to recognize individuals within species.

  8. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs.

    PubMed

    Dufresnes, Christophe; Brelsford, Alan; Béziers, Paul; Perrin, Nicolas

    2014-07-01

    A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.

  9. Development of 10 microsatellite markers from Pantala flavescens and their applicability in studying genetics diversity.

    PubMed

    Cao, Lingzhen; Fu, Xiaowei; Wu, Kongming

    2015-08-01

    Pantala flavescens (Fabricius 1798) is one of the most common species among migration dragonflies. It is often encountered in large swarms during migration or directed dispersal flights. For a better understanding of its gene flow, genetic structure and migration patterns throughout the world, 10 polymorphic microsatellite markers were isolated in this study. We respectively collected 32 P. flavescens from three places (Hunan, Liaoning and Heilongjiang) and 20 P. flavescens from Beijing. Partial genomic libraries containing microsatellite sequences were constructed with magnetic-bead enrichment method. By screening, sequence analysis, PCR amplification and so on, ten 10 polymorphic microsatellite markers were isolated. In order to assess their applicability, genetic diversity of these novel markers was tested in 96 individuals from three populations in China (Hunan, Liaoning and Heilongjiang). These markers were highly polymorphic, with 3-12 alleles per markers. The observed (Ho) and expected (He) heterozygosities ranged 0.321-0.667 and from 0.531 to 0.948 respectively. The genetic difference between Hunan and Liaoning is 0.429, while the genetic difference between Liaoning and Heilongjiang is 0.0508. These microsatellite markers for P. flavescens were developed for the first time, and will be a powerful tool for studying population genetic diversity and dispersal behavior of P. flavescens in China and worldwide.

  10. [A search for null alleles at the microsatellite locus of chum salmon (Oncorhynchus keta Walbaum)].

    PubMed

    Kordicheva, S Iu; Rubtsova, G A; Shitova, M V; Shaĭkhaev, G O; Afanas'ev, K I; Zhivotovskiĭ, L A

    2010-08-01

    Population studies with the use of microsatellite markers face a problem of null alleles, i.e., the absence of a PCR product, caused by the mutations in the microsatellite flanking regions, which serve as the sites of primer hybridization. In this case, the microsatellite primer associated with such mutation is not amplified, leading to false homozygosity in heterozygous individuals. This, in turn, results in biased population genetic estimates, including the excess of homozygotes at microsatellite loci. Analysis of the population structure of a Pacific salmon species, chum salmon (Oncorhynchus keta Walbaum), revealed the presence of null alleles at the Oke3 microsatellite locus in the population samples, in which an excess of homozygotes was observed. The analysis was performed using different combinations of modified primers chosen to match the Oke3 locus. The use of these primers enabled identification of true heterozygotes among those individuals, which were previously diagnosed as homozygotes with the use of standard primers. Removal of null alleles eliminated the excess homozygotes in the chum salmon samples described. In addition to the exclusion of false homozygosity, the use of modified primers makes it possible to introduce polymorphic primer variants associated with certain microsatellite alleles into population studies.

  11. Microsatellite in Aeschynomene falcata (Leguminosae): diversity, cross-amplification, and chromosome localization.

    PubMed

    Polido, C A; Mantello, C C; Moraes, A P; Souza, A P; Forni-Martins, E R

    2014-12-04

    Aeschynomene falcata is an important forage species; however, because of low seed production, it is underutilized as forage species. Aeschynomene is a polyphyletic genus with a challenging taxonomic position. Two subgenera have been proposed, and it is suggested that Aeschynomene can be split in 2 genera. Thus, new markers, such as microsatellite sequences, are desirable for improving breeding programs for A. falcata. Based on transferability and in situ localization, these microsatellite sequences can be applied as chromosome markers in the genus Aeschynomene and closely related genera. Here, we report the first microsatellite library developed for this genus; 11 microsatellites were characterized, with observed and expected heterozygosities ranging from 0.0000 to 0.7143 and from 0.1287 to 0.8360, respectively. Polymorphic information content varied from 0.1167 to 0.7786. The departure from Hardy-Weinberg equilibrium may have resulted from frequent autogamy, which is characteristic of A. falcata. Of the 11 microsatellites, 9 loci were cross-amplified in A. brevipes and A. paniculata and 7 in Dalbergia nigra and Machaerium vestitum. Five of these 7 cross-amplified microsatellites were applied as probes during the in situ hybridization assay and 2 showed clear signals on A. falcata chromosomes, ensuring their viability as chromosome markers.

  12. Response to competition of bulbous geophyte Allium oleraceum differing in ploidy level.

    PubMed

    Fialová, M; Duchoslav, M

    2014-01-01

    Experimental studies that explore the possible causes of ploidy distributions and niche differentiation are rare. Increased competitive ability may be advantageous for survival in dense vegetation and may strongly affect local and regional abundances of cytotypes and potentially contribute to invasion success. We compared survival, growth and reproduction of plants originating from bulbils of three cytotypes (2n = 4x, 5x, 6x) of Allium oleraceum growing with and without a competitor (Arrhenatherum elatius). There was a strong negative effect of competition but no effect of ploidy or ploidy × competition on survivorship, height and total dry mass of A. oleraceum, i.e. no support for different competitive abilities of the ploidy levels. However, slightly different responses of populations to competition treatments within all cytotypes suggest differentiation within cytotypes. Under competition, plant survivorship was low, surviving plants were small, had low dry mass and produced neither sexual nor asexual propagules. Without competition, plant survivorship was high, and cytotypes differed in three traits after 2 year's growth: dry mass of flowers, number of flowers and ratio of the dry mass of sexual to asexual propagules all decreased with increasing ploidy level. We additionally tested tetra- and pentaploids as to whether plants originating from different types of propagule (bulbils, seeds) differ in survivorship, growth and reproduction when growing with and without a competitor. Plants originating from bulbils had higher survivorship, were more robust, flowered earlier and produced more propagules when compared to plants originating from seeds and grown without competition. Under competition, differences in performance between plants originating from seeds and bulbils mostly disappeared, with higher survivorship only for plants originating from bulbils.

  13. Isolation and characterization of microsatellite loci for Florida largemouth bass, Micropterus salmoides floridanus, and other micropterids.

    PubMed

    Lutz-Carrillo, Dijar J; Hagen, Cris; Dueck, Lucy A; Glenn, Travis C

    2008-01-01

    We isolated and characterized 52 novel microsatellite markers from Florida largemouth bass, Micropterus salmoides floridanus, for use in conservation, management and population genetic studies. Markers were assessed in M. s. floridanus from peninsular Florida (n = 30) and averaged eight alleles per locus with observed heterozygosity of 0.57 (range 0-0.97). Cross-taxa amplification was successful among 88% of tested congeners. These polymorphic and potentially taxon-diagnostic markers contribute to the limited number of microsatellites currently available for micropterids and specifically M. s. floridanus.

  14. Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis)

    USGS Publications Warehouse

    Ramey, A.; Graziano, S.L.; Nielsen, J.L.

    2008-01-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. ?? 2007 Blackwell Publishing Ltd.

  15. PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis).

    PubMed

    Ramey, A; Graziano, S L; Nielsen, J L

    2008-03-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco.

  16. Development of nuclear and chloroplast microsatellite markers for the endangered conifer Callitris sulcata (Cupressaceae)1

    PubMed Central

    Sakaguchi, Shota; Lannuzel, Guillaume; Fogliani, Bruno; Wulff, Adrien S.; L’Huillier, Laurent; Kurata, Seikan; Ueno, Saneyoshi; Isagi, Yuji; Tsumura, Yoshihiko; Ito, Motomi

    2015-01-01

    Premise of the study: Microsatellite markers were developed for Callitris sulcata (Cupressaceae), an endangered conifer species in New Caledonia. Methods and Results: Using sequencing by synthesis (SBS) of an RNA-Seq library, 15 polymorphic nuclear and chloroplast microsatellite markers were developed. When evaluated with 48 individuals, these markers showed genetic variations ranging from two to 15 alleles and expected heterozygosity ranging from 0 to 0.881. Conclusions: These markers will be useful for examining the genetic diversity and structure of remaining wild populations and improving the genetic status of ex situ populations. PMID:26312198

  17. Development of microsatellite markers in the tetraploid fern Ceratopteris thalictroides (Parkeriaceae) using RAD tag sequencing.

    PubMed

    Yang, X Y; Long, Z C; Gichira, A W; Guo, Y H; Wang, Q F; Chen, J M

    2016-02-19

    To understand the genetic variability of the tetraploid fern Ceratopteris thalictroides (Parkeriaceae), we described 30 polymorphic microsatellite markers obtained using the restriction site-associated DNA (RAD) tag sequencing technique. A total of 26 individuals were genotyped for each marker. The number of alleles per locus ranged from 4 to 10, and the expected heterozygosity and the Shannon-Wiener index ranged from 0.264 to 0.852 and 0.676 to 2.032, respectively. Because these 30 microsatellite markers exhibit high degrees of genetic variation, they will be useful tools for studying the adaptive genetic variation and sustainable conservation of C. thalictroides.

  18. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    PubMed Central

    Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft

  19. Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

    PubMed Central

    Fonseca, Paulo J.; Amorim, Maria Clara P.

    2015-01-01

    The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. PMID:25653909

  20. Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae).

    PubMed

    Ogrzewalska, M; Bajay, M M; Schwarcz, K; Bajay, S K; Telles, M P C; Pinheiro, J B; Zucchi, M I; Pinter, A; Labruna, M B

    2014-11-14

    Amblyomma aureolatum (Pallas) is the main vector of the bacterium Rickettsia rickettsii, the etiological agent of Brazilian spotted fever. This disease is the most lethal human spotted fever rickettsiosis in the world. Microsatellite loci were isolated from a dinucleotide-enriched library produced from A. aureolatum sampled in Southeastern Brazil. Eight polymorphic microsatellites were further characterized among 38 individuals sampled from São Paulo metropolitan region. The number of observed alleles ranged from 2 to 9, observed heterozygosity was 0.184-0.647, and expected heterozygosity was 0.251-0.747. Cross-species amplifications suggested that these loci will be useful for other Amblyomma species.

  1. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Qi, Haigang; Li, Li; Zhang, Guofan

    2014-01-01

    Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (≥24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

  2. Conserved microsatellites in ants enable population genetic and colony pedigree studies across a wide range of species.

    PubMed

    Butler, Ian A; Siletti, Kimberly; Oxley, Peter R; Kronauer, Daniel J C

    2014-01-01

    Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.

  3. Conserved Microsatellites in Ants Enable Population Genetic and Colony Pedigree Studies across a Wide Range of Species

    PubMed Central

    Butler, Ian A.; Siletti, Kimberly; Oxley, Peter R.; Kronauer, Daniel J. C.

    2014-01-01

    Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups. PMID:25244681

  4. Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives.

    PubMed

    Hempel, K; Peakall, R

    2003-06-01

    The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He +/- SE = 0.58 +/- 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.

  5. Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome.

    PubMed

    Li, Y M; Bai, C Y; Niu, W P; Yu, H; Yang, R J; Yan, S Q; Zhang, J Y; Zhang, M J; Zhao, Z H

    2015-09-28

    Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species.

  6. Heterozygosity increases microsatellite mutation rate

    PubMed Central

    Amos, William

    2016-01-01

    Whole genome sequencing of families of Arabidopsis has recently lent strong support to the heterozygote instability (HI) hypothesis that heterozygosity locally increases mutation rate. However, there is an important theoretical difference between the impact on base substitutions, where mutation rate increases in regions surrounding a heterozygous site, and the impact of HI on sequences such as microsatellites, where mutations are likely to occur at the heterozygous site itself. At microsatellite loci, HI should create a positive feedback loop, with heterozygosity and mutation rate mutually increasing each other. Direct support for HI acting on microsatellites is limited and contradictory. I therefore analysed AC microsatellites in 1163 genome sequences from the 1000 genomes project. I used the presence of rare alleles, which are likely to be very recent in origin, as a surrogate measure of mutation rate. I show that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles. PMID:26740567

  7. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    PubMed Central

    Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

    2001-01-01

    Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

  8. Microsatellite primer development for post oak, Quercus stellata (Fagaceae)1

    PubMed Central

    Chatwin, Warren B.; Carpenter, Kyrie K.; Jimenez, Felix R.; Elzinga, Dave B.; Johnson, Leigh A.; Maughan, Peter J.

    2014-01-01

    • Premise of the study: The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata). This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. • Methods and Results: Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. • Conclusions: We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants. PMID:25309841

  9. Analysis of microsatellites and parentage testing in saltwater crocodiles.

    PubMed

    Isberg, S R; Chen, Y; Barker, S G; Moran, C

    2004-01-01

    Fifteen microsatellite loci were evaluated in farmed saltwater crocodiles for use in parentage testing. One marker (C391) could not be amplied. For the remaining 14, the number of alleles per locus ranged from two to 16, and the observed heterozygosities ranged from 0.219 to 0.875. The cumulative exclusion probability for all 14 loci was .9988. the 11 loci that showed the greatest level of polymorphism were used for parentage testing, with an exclusion probability of .9980. With these 11 markers on 107 juveniles from 16 known breeding pairs, a 5.6% pedigree error rate was detected. This level of pedigree error, if consistent, could have an impact on the accuracy of gentic parameter and breeding value estimation. The usefulness of these markers was also evaluated for assigning parentage in situations where maternity, paternity, or both may not be known. In these situations, a 2% error in parentage assignment was predicted. It is therefore recommended that more micro-satellite markers be used in these situations. The use of these microsatellite markers will broaden the scope of a breeding program, allowing progeny to be tested from adults maintained in large breeding lagoons for selection as future breeding animals.

  10. [Genetic diversity of microsatellite loci in captive Amur tigers].

    PubMed

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten

  11. The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales.

    PubMed

    Wu, Xiaolong; Zhou, Lan; Zhao, Xiangyan; Tan, Zhongyang

    2014-11-01

    Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1-6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes. A total of 63,939 microsatellites and 5825 compound microsatellites were extracted from 56 genomes. It found that GC content has a significant strong correlation with both the counts of microsatellites (CM) and the counts of compound microsatellites (CCM). However, genome size has a moderate correlation only with CM and almost no correlation with CCM. The compound microsatellites occurring in genic regions are obviously more than that in intergenic regions. In general, the number of compound microsatellite decreases with the increase of complexity (C) (the count of individual microsatellites being part of a compound microsatellite) and the complexity hardly exceeds C=4. The vast majority of compound microsatellites exist in intergenic regions, when C≥10. The distributions of SSRs tend to be organism-specific rather than host-specific in herpesvirus genomes. The diversity of microsatellites and compound microsatellites may be helpful for a better understanding of the viral genetic diversity, genotyping, and evolutionary biology in herpesviruses genomes.

  12. A GA microsatellite in the Fli1 promoter modulates gene expression and is associated with systemic lupus erythematosus patients without nephritis

    PubMed Central

    2010-01-01

    Introduction The transcription factor Fli1 is implicated in the pathogenesis of systemic lupus erythematosus (SLE). Recently, a GAn polymorphic microsatellite was characterized in the mouse Fli1 promoter that modulates promoter activity and is truncated in two lupus mouse models compared to non-autoimmune prone mice. In this work, we characterize a homologous GAn microsatellite in the human Fli1 promoter. The purpose of this study is to determine the effect of the microsatellite length on Fli1 promoter activity in vitro and to determine if the length of the GAn microsatellite is associated with SLE and/or specific disease characteristics. Methods Constructs with variable lengths of the GAn microsatellite in the Fli1 promoter were generated and analyzed in promoter/reporter (P/R) assays in a human T cell line. Using three SLE patient cohorts and matched controls, microsatellite length was measured and association with the presence of disease and the occurrence of specific disease manifestations was assessed. Results P/R assays demonstrated that the presence of a shorter microsatellite resulted in higher Fli1 promoter activity. A significant association was observed in the lupus cohort SLE in Gullah Health (SLEIGH) between the GA26 base pair allele and absence of nephritis. Conclusions This study demonstrates that a GAn microsatellite in the human Fli1 promoter is highly polymorphic. The length of the microsatellite is inversely correlated to Fli1 promoter activity in a human T cell line. Although no association between microsatellite length and lupus was observed, an association between a specific microsatellite length and patients without nephritis in the SLEIGH cohort was observed. PMID:21087477

  13. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    PubMed Central

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  14. Characterization of microsatellites in the coding regions

    SciTech Connect

    Tuskan, Gerald A; Li, Shuxian; Yin, Tongming; Wang, Prof. Mingxiu

    2009-01-01

    With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genomewide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs.

  15. Microsatellites Cross-Species Amplification across Some African Cichlids

    PubMed Central

    Bezault, Etienne; Rognon, Xavier; Gharbi, Karim; Baroiller, Jean-Francois; Chevassus, Bernard

    2012-01-01

    The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids. PMID:22701809

  16. Toward fully automated genotyping: genotyping microsatellite markers by deconvolution.

    PubMed Central

    Perlin, M W; Lancia, G; Ng, S K

    1995-01-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. PMID:7485172

  17. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

    PubMed Central

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  18. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    PubMed

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  19. GENETIC VARIATION AND IDENTIFICATION OF PROMISING SOUR CHERRIES INFERRED FROM MICROSATELLITE MARKERS.

    PubMed

    Najafzadeh, R; Arzani, K; Bouzari, N; Saei, A

    2016-01-01

    The aim of this study was to identify the group of highly polymorphic microsatellite markers for identification of promising sour cherries. From among 30 tested microsatellite (SSR) markers, 19 were selected to profile genetic variation in sour cherries due to high polymorphisms. Results indicated a high level of polymorphism of the accessions based on these markers. Totally 148 alleles were generated at 19 SSR loci which 122 alleles were polymorphic. The number of total alleles per locus ranged from 2 to 15 with an average of 7.78 and polymorphism percentage varied from 50 to 100% with an average of 78.76%. Also, PIC varied from 0.47 to 0.89 with an average of 0.79 and heterozygosity ranged from 0.35 to 0.55 with a mean of 0.45. According to these results, these markers specially PMS3, PS12A02, PceGA34, BPPCT021, EMPA004, EMPA018, and Pchgms3 produced good and various levels of amplifications and showed high heterozygosity levels. By the way, the genetic similarity showed a high diversity among the sour cherries. Cluster analysis separated improved cultivars from promising sour cherries, and the PCoA supported the cluster analysis results. Since the studied sour cherries were superior to the improved cultivars and were separated from them in most groups, these sour cherries can be considered as distinct genotypes for further evaluations in the framework of breeding programs and new cultivar identification in cherries. Results also confirmed that the set of microsatellite markers employed in this study demonstrated usefulness of microsatellite markers for the identification of sour cherry genotypes.

  20. Development and characterization of microsatellite markers for Lychnophora pinaster: a study for the conservation of a native medicinal plant.

    PubMed

    Haber, L H; Cavallari, M M; Santos, F R C; Marques, M O M; Gimenes, M A; Zucchi, M I

    2009-05-01

    Lychnophora pinaster Mart. (Asteraceae) is a Brazilian medicinal plant, extensively employed in popular medicine as an anti-inflammatory, analgesic and healing agent. Thirteen polymorphic microsatellite markers were developed and optimized for L. pinaster from an enriched genomic library. The markers were used to analyse 37 plants from two native populations, generating an average number of 6.6 alleles per polymorphic locus. These loci are important tools for future studies of population genetics.

  1. Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos) genome and cross-amplification in other birds

    PubMed Central

    Huang, Yinhua; Tu, Jianfeng; Cheng, Xuebo; Tang, Bo; Hu, Xiaoxiang; Liu, Zhaoliang; Feng, Jidong; Lou, Yankun; Lin, Li; Xu, Ke; Zhao, Yulong; Li, Ning

    2005-01-01

    In order to study duck microsatellites, we constructed a library enriched for (CA)n, (CAG)n, (GCC)n and (TTTC)n. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97) was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04) at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%). The polymorphism information content (PIC) of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose. PMID:15943922

  2. Isolation and characterization of novel microsatellite loci for the endangered orchid Cypripedium japonicum (Orchidaceae)1

    PubMed Central

    Yamashita, Yumi; Izuno, Ayako; Isagi, Yuji; Kurosawa, Takahide; Kaneko, Shingo

    2016-01-01

    Premise of the study: Twenty-six microsatellite markers were developed for the endangered orchid Cypripedium japonicum (Orchidaceae) to estimate the clonal diversity and genetic structure of the remaining populations in Japan. Methods and Results: Microsatellite loci of C. japonicum were isolated using Ion Personal Genome Machine (PGM) sequencing. The primer sets were tested on 55 ramets sampled from two populations in Japan. Sixteen loci showed polymorphism in at least one population, with two to five alleles per locus. Observed and expected heterozygosities for the two populations ranged from 0.00 to 0.92 and 0.00 to 0.71, respectively. Conclusions: The microsatellite markers developed here provide a useful tool to analyze clonal structure and sexual regeneration status and will help to manage the remaining genetic variation within C. japonicum. PMID:26949576

  3. Development of microsatellite markers for Suriana maritima (Surianaceae) using next-generation sequencing technology.

    PubMed

    Chen, W S; Zhao, G; Jian, S G; Wang, Z F

    2015-10-30

    Our objective was to develop microsatellite markers for use in assessing genetic variation in the small shrub or tree species Suriana maritima (Surianaceae). In China, this species is found only as a few fragmented populations and individuals on the Paracel Islands. Using next-generation genome sequencing methodology, we developed 17 novel microsatellite markers for S. maritima. Fifty-four individuals from six populations of S. maritima were examined for polymorphisms; only one allele was detected for each of the markers. Microsatellite loci developed indicate a complete absence of genetic diversity for S. maritima on the Paracel Islands in China. These markers will be useful for examining genetic variation among S. maritima populations in other areas of the world.

  4. Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae).

    PubMed

    Ossa, Carmen G; Larridon, Isabel; Peralta, Gioconda; Asselman, Pieter; Pérez, Fernanda

    2016-12-01

    The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with FST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.

  5. Development and characterization of microsatellite loci for Lindera glauca (Lauraceae)1

    PubMed Central

    Xiong, Biao; Dong, Shubin; Qi, Ji; Zhang, Limei; Ha, Denglong; Zhang, Zhixiang

    2016-01-01

    Premise of the study: Microsatellite primers were developed to investigate population genetic structure in Lindera glauca (Lauraceae). Methods and Results: Twenty-five microsatellite primers were developed and optimized for L. glauca using Illumina’s Solexa sequencing technology. These novel primers were found to be polymorphic in nine wild L. glauca populations with 81 total alleles confirmed and genotyped via capillary gel electrophoresis. The total number of alleles, observed heterozygosity, and expected heterozygosity for each population ranged from one to four, from 0.00 to 0.90, and from 0.00 to 0.79, respectively. In addition, the 25 primers were tested in 10 additional individuals of the related species L. communis, and all but four markers showed good amplification results. Conclusions: This set of microsatellite primers is the first specifically developed for L. glauca and will facilitate studies of genetic diversity and evolution among populations of this species. PMID:27843729

  6. Characterization of microsatellite markers in two exploited African trees, Entandrophragma candollei and E. utile (Meliaceae)1

    PubMed Central

    Monthe, Franck S.; Duminil, Jérôme; Tosso, Félicien; Migliore, Jérémy; Hardy, Olivier J.

    2017-01-01

    Premise of the study: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae). Methods and Results: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively. The number of alleles ranged from two to 17 for E. candollei and from three to 19 for E. utile. Mean expected and observed heterozygosity ranged between 0.75 ± 0.13 and 0.55 ± 0.23 for E. candollei and between 0.73 ± 0.10 and 0.49 ± 0.2 for E. utile. Conclusions: These sets of nuclear microsatellite markers constitute useful tools for exploring gene flow patterns in these two Entandrophragma species. PMID:28224058

  7. Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics

    PubMed Central

    Sun, Kaiyan; Chang, Dan; Bai, Shiqie; Shen, Yixin; Huang, Linkai; Zhang, Jin; Zhang, Yu; Dong, Yanhai

    2016-01-01

    Erianthus arundinaceus is not only an important germplasm resource for sugarcane breeding but also a potential bioenergy plant. Making clear the distribution of the chromosome ploidy of wild E. arundinaceus in china is the premise of the research and utilization of this species. Therefore, the objectives of this study were to determine the ploidy level and DNA content of the 55 E. arundinaceus accessions using flow cytometry and to identify the correlation between ploidy and phenotypic traits. Among the 55 accessions, four tetraploids and 51 hexaploids were identified. The four tetraploids originated from Mengma Yunnan, Shuangjiang Yunnan, Gaozhou Guangdong and Chengle Sichuan. The mean DNA content was 4.82 pg/2C for the tetraploid and 7.30 pg/2C for the hexaploid plants. The ploidy was negatively correlated with cellulose content and positively correlated (P<0.05) with plant height, stem diameter, leaf width, dry weight per plant, fresh weight per plant and hemicellulose content. However, ploidy was not correlated with leaf length, tiller number and the ratio of dry weight and fresh weight. This study will be useful for revealing the distribution of the ploidy of wild E. arundinaceus in Chin, traits markers analysis, and utilization of this species, such as cultivar improvement and sugarcane breeding in the future. PMID:27010798

  8. Development of microsatellites from Fothergilla ×intermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae1

    PubMed Central

    Hatmaker, E. Anne; Wadl, Phillip A.; Mantooth, Kristie; Scheffler, Brian E.; Ownley, Bonnie H.; Trigiano, Robert N.

    2015-01-01

    Premise of the study: We developed microsatellites from Fothergilla ×intermedia to establish loci capable of distinguishing species and cultivars, and to assess genetic diversity for use by ornamental breeders and to transfer within Hamamelidaceae. Methods and Results: We sequenced a small insert genomic library enriched for microsatellites to develop 12 polymorphic microsatellite loci. The number of alleles detected ranged from four to 15 across five genera within Hamamelidaceae. Shannon’s information index ranged from 0.07 to 0.14. Conclusions: These microsatellite loci provide a set of markers to evaluate genetic diversity of natural and cultivated collections and assist ornamental plant breeders for genetic studies of five popular genera of woody ornamental plants. PMID:25909044

  9. Development of 18 novel microsatellite primers for Begonia fimbristipula (Begoniaceae), an endangered medicinal plant in China1

    PubMed Central

    Zhao, Bo; Du, Yun-Qian; Li, Jing-Jian; Tang, Wen-Xiu; Zhong, Shu-Hua

    2016-01-01

    Premise of the study: Begonia fimbristipula (Begoniaceae) is a medicinal herb distributed in the Chinese provinces of Fujian, Guangdong, Guangxi, Hainan, Hunan, Jiangxi, and Zhejiang, and it is on the verge of extinction due to habitat destruction and deterioration of its ecosystem. Here we developed a set of highly polymorphic microsatellite markers for population genetic and conservation studies of this endangered medicinal plant. Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 18 polymorphic microsatellite markers were identified within 48 individuals from two geographic locations. The observed and expected heterozygosities ranged from 0.208 to 1.000 and from 0.291 to 0.812, respectively. These microsatellite markers were cross-amplified in five related Begonia species, and six loci were successfully amplified in all species. Conclusions: These 18 markers will be useful for better conservation and utilization of wild resources of B. fimbristipula and other Begonia species in the future. PMID:27437176

  10. FLASH and NPAT positive but not Coilin positive Cajal Bodies correlate with cell ploidy.

    PubMed

    Bongiorno-Borbone, Lucilla; De Cola, Antonella; Vernole, Patrizia; Finos, Livio; Barcaroli, Daniela; Knight, Richard A; Melino, Gerry; De Laurenzi, Vincenzo

    2008-08-01

    Cajal Bodies are one of many specialised organelles contained in the eukaryotic cell nucleus, and are involved in a number of functions, including regulation of replication-dependent histone gene transcription. In normal diploid cells their number varies between 0 and 4 depending on the cell cycle phase, although in cancer cell lines their number is extremely variable and it has been suggested that it correlates with cell ploidy. Here we show that in mammalian cells, as in Drosophila, two distinct though functionally related bodies exist: a histone gene locus body and a Cajal Body. The first one can be detected using FLASH or NPAT as markers while the second is labelled using antibodies against Coilin. Only the number of FLASH/NPAT histone gene locus bodies correlates with ploidy and only these organelles appear to be regulated during the cell cycle. Finally, we show that the two organelles completely co-localize during the S phase of the cell cycle.

  11. Nuclear ploidy of neonatal rat livers: effects of two hepatic carcinogens (mirex and dimethylnitrosamine)

    SciTech Connect

    Carlson, J.; Abraham, R.

    1985-01-01

    The effect of two hepatic carcinogens, dimethylnitrosamine (DMN) (genotoxic) and mirex (epigenetic), on polyploidization in 12-d-old neonatal rats was investigated by Coulter counteranalysis and (/sup 3/H) thymidine uptake in isolated hepatic nuclear classes. DMN disturbed the normal ploidy development in the neonatal liver and the proportion of nuclei in the ploidy classes by inducing the premature formation of a significant population of tetraploids with a concommitant reduction in diploids. A great proportion of the replicative activity was present in tetraploid nuclei as measured by the incorporation of (/sup 3/H) thymidine. The labeling index and number of mitoses were also increased. In contrast to DMN, mirex had no influence on polyploidization. The neonatal rats used in these studies thus offer an opportunity to investigate in vivo the mode of action of genotoxic versus epigenetic compounds with reference to their effect on DNA.

  12. A novel microsatellite control system

    SciTech Connect

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1998-02-01

    The authors are researching extremely simple yet quite capable analog pulse-coded neural networks for ``smaller-faster-cheaper`` spacecraft attitude and control systems. The will demonstrate a prototype microsatellite that uses their novel control method to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source. Though still in design infancy, the ``Nervous Net`` controllers described could allow for space missions not currently possible given conventional satellite hardware. Result, prospects and details are presented.

  13. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

    PubMed

    Zapiola, Maria L; Cronn, Richard C; Mallory-Smith, Carol A

    2010-07-01

    We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape level study of gene flow from transgenic glyphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of transgenic pollen both within the Agrostis complex and the related genera Polypogon.

  14. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP) -based assays. Despite domestic and international demands fr...

  15. Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies.

    PubMed

    Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E; Garibaldi, Lucas A; Irisarri, J Gonzalo N; Saloniemi, Irma; Saikkonen, Kari

    2016-01-01

    Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

  16. Distribution and ecological consequences of ploidy variation in Artemisia sieberi in Iran

    NASA Astrophysics Data System (ADS)

    Jalili, Adel; Rabie, Mina; Azarnivand, Hossein; Hodgson, John G.; Arzani, Hossein; Jamzad, Ziba; Asri, Younes; Hamzehee, Behnam; Ghasemi, Farzaneh; Hesamzadeh Hejazi, S. M.; Abbas-Azimi, R.

    2013-11-01

    Because of their high proportion in the plant kingdom polyploid taxa are considered to have had evolutionary advantages over their diploid ancestors. These advantages may have included new characteristics that enable polyploids to occupy a broader range of habitats. In this context, we assess the ecological range of Artemisia sieberi, a canopy dominant within an important vegetation type in Iran. We assess the extent to which ploidy covaries with geographical and ecological distribution and look for ecologically-significant differences in the functional characteristics of diploids and polyploids. Populations of A. sieberi were sampled widely in Iran and soil characteristics, climate and anatomical and phytochemical plant attributes were measured. Also, in parallel, an independent genetic assessment of populations was carried out using genetic fingerprinting. Two ploidy levels were identified: 75% of the 34 populations of A. sieberi populations sampled were tetraploid (2n = 4x = 36) with the remainder diploid (2n = 2x = 18). Plants of differing ploidy also differed anatomically, genetically and chemically. Tetraploid populations had larger cells and lower stomatal densities and a different essential oil composition. They also appear ecologically distinct, occupying more fertile, mesic habitats than diploids. Genetic fingerprinting revealed the existence of two genetically differentiated subgroups independent of ploidy but with some geographic and ecological pattern. We conclude that diploids and tetraploids have a different ecological distribution and that the absence of mixed diploid-tetraploid populations is a reflection of differing fitness in different habitats. We suspect that a key ecological difference between diploids and tetraploids is the increased stomatal size of tetraploids, possibly resulting from the increased genome and hence cell size following polyploidisation. Polyploid-formation may be constrained in arid habitats by problems of water

  17. Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies

    PubMed Central

    Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E.; Garibaldi, Lucas A.; Irisarri, J. Gonzalo N.; Saloniemi, Irma; Saikkonen, Kari

    2016-01-01

    Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

  18. Gene flow among populations of two rare co-occurring fern species differing in ploidy level.

    PubMed

    Bucharová, Anna; Münzbergová, Zuzana

    2012-01-01

    Differences in ploidy levels among different fern species have a vast influence on their mating system, their colonization ability and on the gene flow among populations. Differences in the colonization abilities of species with different ploidy levels are well known: tetraploids, in contrast to diploids, are able to undergo intra-gametophytic selfing. Because fertilization is a post-dispersal process in ferns, selfing results in better colonization abilities in tetraploids because of single spore colonization. Considerably less is known about the gene flow among populations of different ploidy levels. The present study examines two rare fern species that differ in ploidy. While it has already been confirmed that tetraploid species are better at colonizing, the present study focuses on the gene flow among existing populations. We analyzed the genetic structure of a set of populations in a 10×10 km study region using isoenzymes. Genetic variation in tetraploid species is distributed mainly among populations; the genetic distance between populations is correlated with the geographical distance, and larger populations host more genetic diversity than smaller populations. In the diploid species, most variability is partitioned within populations; the genetic distance is not related to geographic distance, and the genetic diversity of populations is not related to the population size. This suggests that in tetraploid species, which undergo selfing, gene flow is limited. In contrast, in the diploid species, which experience outcrossing, gene flow is extensive and the whole system behaves as one large population. Our results suggest that in ferns, the ability to colonize new habitats and the gene flow among existing populations are affected by the mating system.

  19. Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex.

    PubMed

    Lin, Yaping; Chen, Yiyong; Xiong, Wei; Zhan, Aibin

    2016-05-01

    The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene-associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24-48), and Cape Town, South Africa (N = 24-33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C. intestinalis as a model.

  20. Flow cytometric analysis of DNA ploidy and cell proliferation activity in colorectal carcinoma.

    PubMed

    Mazzei, T; Tonelli, F; Mini, E; Mazzoni, P; Pesciullesi, A; Valanzano, R; Ficari, F; Biondi, C; Periti, P

    1995-01-01

    The aim of this study was to evaluate the relationship between DNA ploidy, proliferative activity and other prognostic factors and the survival of patients with colorectal cancer. 45 patients were prospectively investigated for 6 years. Fresh multiple samples for flow cytometric analysis of DNA content were collected during surgical resection of primary tumor. A 42% frequency of aneuploidy was observed with a median DNA index value of 1.54. The proliferative activity (%S+G2M cells) was higher in the aneuploid cell sub-population (28.6%) compared to the diploid counterpart (22.7%)(p = 0.05). No significant relationship between DNA ploidy and tumor site, Dukes' stage, histological type, grading age or sex was observed. No correlation between DNA ploidy and survival was demonstrated, including in the analysis of patient subsets according to stage. No additive prognostic information was obtained from a breakdown analysis as a function of DI values, percentages of aneuploid cells and proliferative activity. This study suggests that flow cytometric content analysis lacks prognostic value in colorectal carcinoma.

  1. Assessment of ploidy stability of the somatic embryogenesis process in Quercus suber L. using flow cytometry.

    PubMed

    Loureiro, J; Pinto, G; Lopes, T; Dolezel, J; Santos, C

    2005-08-01

    Flow cytometry analyses were used to verify the ploidy stability of Quercus suber L. somatic embryogenesis process. Leaf explants of two adult cork oak trees (QsG0 and QsG5) of the North of Portugal were inoculated on MS medium with 2,4-D and zeatin. After 3 months, calluses with embryogenic structures were isolated and transferred to fresh MS medium without growth regulators and somatic embryo evolution was followed. Morphologically normal somatic embryos (with two cotyledons) and abnormal somatic embryos (with one or three cotyledons) were used in this assay. Flow cytometry combined with propidium iodide staining was employed to estimate DNA ploidy levels and nuclear DNA content of somatic embryos and leaves from mother plants. No significant differences (P< or =0.05) were detected among embryos, and between the embryos and the mother plants. Also, after conversion of these embryos, no significant morphological differences were observed among the somatic embryo-derived plants. These results and further studies using converted plantlet leaves and embryogenic callus tissue indicate that embryo cultures and converted plantlets were stable with regard to ploidy level. As no major somaclonal variation was detected our primary goal of "true-to-type" propagation of cork oak using somatic embryogenesis was assured at this level. The estimation of the 2C nuclear DNA content for this species is similar to the previously obtained value.

  2. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass

    PubMed Central

    Grabowski, Paul P; Morris, Geoffrey P; Casler, Michael D; Borevitz, Justin O

    2014-01-01

    Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass. PMID:24962137

  3. Why only tetraploid Solidago gigantea (Asteraceae) became invasive: a common garden comparison of ploidy levels.

    PubMed

    Schlaepfer, Daniel R; Edwards, Peter J; Billeter, Regula

    2010-07-01

    Many studies have compared the growth of plants from native and invasive populations, but few have considered the role of ploidy. In its native range in North America, Solidago gigantea Aiton (Asteraceae) occurs as a diploid, tetraploid and hexaploid, with considerable habitat differentiation and geographic separation amongst these ploidy levels. In the introduced range in Europe, however, only tetraploid populations are known. We investigated the growth performance and life history characteristics of plants from 12 European and 24 North American (12 diploid, 12 tetraploid) populations in a common garden experiment involving two nutrient and two calcium treatments. Twelve plants per population were grown in pots for two seasons. We measured 24 traits related to leaf nutrients, plant size, biomass production and phenology as well as sexual and vegetative reproduction. Native diploid plants had a higher specific leaf area and higher leaf nutrient concentrations than native tetraploids, but tetraploids produced many more shoots and rhizomes. Diploids grown with additional calcium produced less biomass, whereas tetraploids were not affected. European plants were less likely to flower and produced smaller capitulescences than North American tetraploids, but biomass production and shoot and rhizome number did not differ. We conclude that a knowledge of ploidy level is essential in comparative studies of invasive and native populations. While clonal growth is important for the invasion success of tetraploid S. gigantea, its potential was not acquired by adaptation after introduction but by evolutionary processes in the native range.

  4. Role of ploidy in cadmium and nickel uptake by Matricaria chamomilla plants.

    PubMed

    Kovácik, Jozef; Klejdus, Borivoj; Grúz, Jirí; Malcovská, Silvia; Hedbavny, Josef

    2010-01-01

    Cadmium and nickel uptake by diploid and tetraploid chamomile (Matricaria chamomilla L.) cultivars (Novbona and Lutea, respectively) exposed to 60 microM solutions of individual metals over 7 days was studied. Diploid plants accumulated higher amount of Cd in both shoots and roots compared to tetraploid plants while Ni accumulation was ploidy-independent. Cd presence caused higher accumulation of total soluble phenols and flavonoids and higher phenylalanine ammonia-lyase and guaiacol-peroxidase activities in diploid cultivar in comparison with tetraploid but phenolic acids did not show direct correlation with metal accumulation and even decreased in the leaves of Ni-exposed plants. Lignin content was preferentially elevated in the roots of diploid cultivar. Among 17 free amino acids, their sum increased mainly in the leaves of Cd-exposed plants (owing to increase in serine, alanine and proline). Potassium decrease in both cultivars in response to Cd was ploidy-independent and Ca, Mg and Fe accumulation were almost unaffected. It is concluded that Cd accumulation in chamomile may be mediated by the accumulation of phenols but they have no active role in shoot Ni accumulation. Present findings in the context of our previous studies and limited available literature about ploidy effect on metal accumulation are discussed.

  5. A general ploidy model for the evolution of helping in viscous populations.

    PubMed

    Yeh, Angela Yi-Chen; Gardner, Andy

    2012-07-07

    There is growing interest in understanding how kin selection drives the evolution of social behaviours in viscous populations. A key result, that has inspired much work on this topic, is the exact cancellation of the genetic relatedness and kin competition effects of dispersal in the simplest models of population viscosity, such that a reduction in the rate of dispersal neither promotes nor inhibits the evolution of helping behaviour. This theoretical result has been demonstrated for populations characterised by haploid, diploid and haplodiploid modes of inheritance. Here we develop a model of general ploidy that recovers these three scenarios as special cases and allows examination of scenarios that have not been considered previously. Specifically, we: clarify the importance of the implicit assumption of monandry in previous models; show that the cancellation result obtains in some models of ploidy but not in others; and reveal that the cancellation result obtains for different reasons in different models of ploidy. The cancellation result therefore hinges upon a population's genetic system as well as its demography.

  6. Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast

    PubMed Central

    Chan, CSM.; Botstein, D.

    1993-01-01

    We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it allows detection of a gain of the marked chromosomes even if there is a gain of the entire set of chromosomes (increase-in-ploidy). This assay was used to screen for chromosome-gain or increase-in-ploidy mutants. Five complementation groups have been defined for recessive mutations that confer an increase-in-ploidy (ipl) phenotype, which, in each case, cosegregates with a temperature-sensitive growth phenotype. Four new alleles of CDC31, which is required for spindle pole body duplication, were also recovered from this screen. Temperature-shift experiments with ipl1 cells show that they suffer severe nondisjunction at 37°. Similar experiments with ipl2 cells show that they gain entire sets of chromosomes and become arrested as unbudded cells at 37°. Molecular cloning and genetic mapping show that IPL1 is a newly identified gene, whereas IPL2 is allelic to BEM2, which is required for normal bud growth. PMID:8293973

  7. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats.

    PubMed

    Kelkar, Yogeshwar D; Strubczewski, Noelle; Hile, Suzanne E; Chiaromonte, Francesca; Eckert, Kristin A; Makova, Kateryna D

    2010-01-01

    Microsatellites are abundant in eukaryotic genomes and have high rates of strand slippage-induced repeat number alterations. They are popular genetic markers, and their mutations are associated with numerous neurological diseases. However, the minimal number of repeats required to constitute a microsatellite has been debated, and a definition of a microsatellite that considers its mutational behavior has been lacking. To define a microsatellite, we investigated slippage dynamics for a range of repeat sizes, utilizing two approaches. Computationally, we assessed length polymorphism at repeat loci in ten ENCODE regions resequenced in four human populations, assuming that the occurrence of polymorphism reflects strand slippage rates. Experimentally, we determined the in vitro DNA polymerase-mediated strand slippage error rates as a function of repeat number. In both approaches, we compared strand slippage rates at tandem repeats with the background slippage rates. We observed two distinct modes of mutational behavior. At small repeat numbers, slippage rates were low and indistinguishable from background measurements. A marked transition in mutability was observed as the repeat array lengthened, such that slippage rates at large repeat numbers were significantly higher than the background rates. For both mononucleotide and dinucleotide microsatellites studied, the transition length corresponded to a similar number of nucleotides (approximately 10). Thus, microsatellite threshold is determined not by the presence/absence of strand slippage at repeats but by an abrupt alteration in slippage rates relative to background. These findings have implications for understanding microsatellite mutagenesis, standardization of genome-wide microsatellite analyses, and predicting polymorphism levels of individual microsatellite loci.

  8. Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations.

    PubMed

    Kirst, M; Cordeiro, C M; Rezende, G D S P; Grattapaglia, D

    2005-01-01

    We report the genetic analysis of 192 unrelated individuals of an elite breeding population of Eucalyptus grandis (Hill ex Maiden) with a selected set of six highly polymorphic microsatellite markers developed for species of the genus Eucalyptus. A full characterization of this set of six loci was carried out generating allele frequency distributions that were used to estimate parameters of genetic information content of these loci, including expected heterozygosity, polymorphism information content (PIC), power of exclusion, and probability of identity. The number of detected alleles per locus ranged from 6 to 33, with an average of 19.8 +/- 9.2. The average expected heterozygosity was 0.86 +/- 0.11 and the average PIC was 0.83 +/- 0.16. Using only three loci, it was possible to discriminate all 192 individuals. The overall probability of identity considering all six EMBRA microsatellite markers combined was lower than 1 in 2 billion. An analysis of the sample size necessary to estimate expected heterozygosity with minimum variance indicated that at least 64 individuals have to be genotyped to characterize this parameter with adequate accuracy for most microsatellites in Eucalyptus. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing.

  9. Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera.

    PubMed

    Miz, R B; Tacuatiá, L O; Cidade, F W; de Souza, A P; Bered, F; Eggers, L; de Souza-Chies, T T

    2016-09-16

    Recent phylogenetic studies on Sisyrinchium strongly suggest that species classified in section Hydastylus and section Viperella belong to a single group of plants in recent adaptive radiation (Clade IV). These species neither present clear morphological differentiation among them nor show clear identification using DNA barcode markers. Thus, the main goal of this study was to develop a set of polymorphic microsatellite markers compatible for representative species of both sections to ensure variability that could be revealed by SSR markers. Therefore, microsatellite primers were isolated and characterized for Sisyrinchium palmifolium and S. marchioides. In addition, transferability of the developed primers was tested in Iridoideae, primarily in closely related species of Sisyrinchium. Sixteen microsatellite loci were developed from enriched genomic libraries, of which ten were polymorphic. GST values indicated higher differentiation among subpopulations of S. palmifolium than those from S. marchioides. Major transferability was obtained using primers isolated from S. marchioides. All primers exhibited higher rates of cross-amplification for species belonging to Clade IV of Sisyrinchium, as well as to the genera Calydorea and Herbertia. These developed microsatellite markers can be used as an efficient tool for characterization of genetic variability in species belonging to Iridoideae, as well as for studies on population dynamics, genetic structure, and mating system in other Sisyrinchium species.

  10. Isolation, characterization, and multiplexing of novel microsatellite markers for the tropical scalloped spiny lobster (Panulirus homarus).

    PubMed

    Delghandi, M; Goddard, S; Jerry, D R; Dao, H T; Afzal, H; Al-Jardani, S S

    2015-12-29

    Of the various spiny lobster species in the tropical and subtropical Indo-West Pacific region, the tropical scalloped spiny lobster (Panulirus homarus) supports one of the most commercially valuable fishery resources in many coastal African and Asian countries. The last decade has witnessed a serious decline in the wild populations of this species. Knowledge of the genetic basis of spiny lobster population structure is a prerequisite to achieve a sustainable fisheries management for this species. Here, we describe 13 novel polymorphic microsatellite markers developed for P. homarus, using a cross-species primer design strategy based on P. ornatus Roche 454 shot-gun generated sequencing. Microsatellite polymorphisms were assessed in 96 unrelated P. homarus individuals of a natural population, with the number of alleles per locus varying from 2 to 14, the observed and expected heterozygosity from 0.00 to 0.78 and from 0.03 to 0.79, respectively, and with only four loci (Pho-G27, Pho-G32, Pho-G36, and Pho-G58) deviating from Hardy- Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between loci Pho-G22 - Pho-G30, and Pho-G30 - Pho-G35. The successful cross amplification of these microsatellites highlights the potential of the developed microsatellites for future population genetic research within the different Panulirus species.

  11. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development

    PubMed Central

    Wang, Biao; Ekblom, Robert; Castoe, Todd A.; Jones, Eleanor P.; Kozma, Radoslav; Bongcam-Rudloff, Erik; Pollock, David D.; Höglund, Jacob

    2012-01-01

    The black grouse (Tetrao tetrix) is a galliform bird species that is important for both ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species. PMID:22724064

  12. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

    PubMed

    Wang, Biao; Ekblom, Robert; Castoe, Todd A; Jones, Eleanor P; Kozma, Radoslav; Bongcam-Rudloff, Erik; Pollock, David D; Höglund, Jacob

    2012-04-01

    The black grouse (Tetrao tetrix) is a galliform bird species that is important for both ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.

  13. Development and characterization of 32 microsatellite loci in Genipa americana (Rubiaceae)1

    PubMed Central

    Manoel, Ricardo O.; Freitas, Miguel L. M.; Barreto, Mariana A.; Moraes, Mário L. T.; Souza, Anete P.; Sebbenn, Alexandre M.

    2014-01-01

    • Premise of the study: Microsatellite primers were developed for the tree species Genipa americana (Rubiaceae) for further population genetic studies. • Methods and Results: We identified 144 clones containing 65 repeat motifs from a genomic library enriched for (CT)8 and (GT)8 motifs. Primer pairs were developed for 32 microsatellite loci and validated in 40 individuals of two natural G. americana populations. Seventeen loci were polymorphic, revealing from three to seven alleles per locus. The observed and expected heterozygosities ranged from 0.24 to 1.00 and from 0.22 to 0.78, respectively. • Conclusions: The 17 primers identified as polymorphic loci are suitable to study the genetic diversity and structure, mating system, and gene flow in G. americana. PMID:25202610

  14. Development and characterization of microsatellite markers for the Chinese endangered medicinal plant Tetrastigma hemsleyanum.

    PubMed

    Wang, Y H; Chen, N; Zhang, Y C; Fu, C X

    2014-10-31

    Tetrastigma hemsleyanum (Vitaceae) is an endangered medicinal plant endemic to China. Because of its widely known efficacy for treating many health problems, wild resources of this species are currently undergoing a rapid decline. Few studies have been conducted examining the population genetics or development of microsatellite loci for this plant. In this study, 14 microsatellite loci were isolated and characterized for T. hemsleyanum using a double-suppression PCR method. Polymorphisms were tested with a total of 50 individuals from 2 natural populations. The number of alleles per locus ranged from 3-9, with an average of 7 alleles per locus. The observed and expected heterozygosity per locus ranged from 0-1 and from 0.068-0.803, respectively. The polymorphism information content value varied from 0.215-0.760. These loci may facilitate further genetic studies of populations of T. hemsleyanum and provide guidance for their conservation.

  15. Characterization of microsatellite loci for an Australian epiphytic orchid, Dendrobium calamiforme, using illumina sequencing

    DOE PAGES

    Trapnell, Dorset W.; Beasley, Rochelle R.; Lance, Stacey L.; ...

    2015-06-05

    Our premise describes how microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ~80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. In conclusion, these novel markers will serve as valuable tools for investigation ofmore » levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history.« less

  16. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms

    PubMed Central

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-01-01

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes. PMID:24296905

  17. Microsatellite marker development for the coastal dune shrub Prunus maritima (Rosaceae)1

    PubMed Central

    Badgley, Emily M.; Grubisha, Lisa C.; Roland, Anna K.; Connolly, Bryan A.; Klooster, Matthew R.

    2015-01-01

    • Premise of the study: Microsatellite primers were developed in the beach plum, Prunus maritima, to investigate the genetic composition of remaining populations in need of conservation and, in future studies, to determine its relation to P. maritima var. gravesii. • Methods and Results: Fourteen primer pairs were identified and tested in four populations throughout the species’ geographic range. Of these 14 loci, 12 were shown to be polymorphic among a total of 60 P. maritima individuals sampled (15 individuals sampled from four populations). Among the polymorphic loci, the number of alleles ranged from two to 10 and observed heterozygosity of loci ranged from 0.07 to 0.93 among specimens tested. • Conclusions: These microsatellites will be useful in evaluating the population genetic composition of P. maritima and in developing approaches for further conservation and management of this species within the endangered coastal dune ecosystem of the northeastern United States. PMID:25699222

  18. Development and characterization of microsatellite loci in the mistletoe Psittacanthus schiedeanus (Loranthaceae)1

    PubMed Central

    González, Clementina; Harvey, Nick; Ornelas, Juan Francisco

    2015-01-01

    • Premise of the study: Microsatellite primers were developed for the parasitic Psittacanthus schiedeanus, a common mistletoe species on cloud forest–adapted tree hosts in Mesoamerica, to investigate intraspecific genetic patterns of diversity and genetic structure. • Methods and Results: Using an enriched library, 10 polymorphic microsatellite loci were developed in P. schiedeanus. All loci consisted of dinucleotide repeats. Average alleles per locus were 12 (4–17), and a total of 120 alleles were recorded across 39 individuals from four populations in Mexico. Primers were tested in 11 additional species, but only amplified successfully in P. calyculatus and P. angustifolius. • Conclusions: The polymorphic loci described will be useful in studies of genetic diversity and genetic population differentiation in natural populations of these parasitic plants, and will provide valuable information to understand the importance of host distribution. PMID:25606357

  19. Development and characterization of microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla.

    PubMed

    Kollars, Nicole M; Krueger-Hadfield, Stacy A; Byers, James E; Greig, Thomas W; Strand, Allan E; Weinberger, Florian; Sotka, Erik E

    2015-01-01

    Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid-diploid primary producer.

  20. Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla

    PubMed Central

    Byers, James E.; Greig, Thomas W.; Strand, Allan E.; Weinberger, Florian

    2015-01-01

    Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer. PMID:26339541

  1. Isolation and characterization of microsatellite loci for Smilax sieboldii (Smilacaceae)1

    PubMed Central

    Ru, Yalu; Cheng, Ruijing; Shang, Jing; Zhao, Yunpeng; Li, Pan; Fu, Chengxin

    2017-01-01

    Premise of the study: Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. Methods and Results: Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S. sieboldii. The number of alleles per locus ranged from four to 18; the expected heterozygosity ranged from 0.59 to 0.92. Twelve loci were successfully amplified in five related species: S. scobinicaulis, S. californica, S. hispida, S. moranensis, and S. jalapensis. Conclusions: These novel expressed sequence tag–derived microsatellite markers will facilitate further population genetic research of S. sieboldii and its close allies of the S. hispida group. PMID:28337395

  2. Development and characterization of microsatellite loci for the endangered scrub Lupine, Lupinus aridorum (Fabaceae)

    DOE PAGES

    Ricono, Angela; Bupp, Glen; Peterson, Cheryl; ...

    2015-04-01

    Microsatellite primers were developed in scrub lupine (Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [L. diffusus] and Gulf Coast lupine [L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. In conclusion, these loci are the first developed for Florida species of lupine and will be used tomore » determine differentiation among species and to aid in conservation of the endangered scrub lupine.« less

  3. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    PubMed

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-04

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  4. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    PubMed Central

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  5. Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae).

    PubMed

    Badri, Mounawer; Zitoun, Adel; Ilahi, Houcine; Huguet, Thierry; Aouani, Mohamed Elarbi

    2008-12-01

    Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with Q(ST) = 0.47, and F(ST) = 0.47 for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of Q(ST) and F(ST). Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P(2)0(5)) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, He, were established in five microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.

  6. Assessment of microsatellites in estimating inter- and intraspecific variation among Neotropical Crocodylus species.

    PubMed

    Bashyal, A; Gross, B A; Venegas-Anaya, M; Lowrance, F; Densmore Iii, L D

    2014-07-25

    We tested microsatellites that were developed for the saltwater crocodile (Crocodylus porosus) for cross-species amplification and to provide an estimate of inter- and intraspecific variation among four species of Neotropical crocodiles (C. rhombifer, C. intermedius, C. acutus, and C. moreletii). Our results indicated that with the exception of 2 loci in C. intermedius, all 10 microsatellite loci were successfully amplified in the 4 species, producing a set of variably sized alleles that ranged in number between 2 and 14 alleles per locus. Similarly, private alleles (i.e., unique alleles) also were reported in all 4 species for at least 3 loci. The mean observed and expected heterozygosities (averaged across species for all 10 loci combined) ranged from 0.39 to 0.77 and from 0.44 to 0.78, respectively. In addition to this, we evaluated these microsatellites in 2 populations of C. acutus and C. moreletii to assess their utility in estimating intraspecific levels of polymorphisms. These microsatellites also showed considerable allelic variation in population level analysis. The set of 10 microsatellite loci in our study had the potential to be used as a tool in population and conservation genetic studies of Neotropical crocodiles.

  7. Development, inheritance, and linkage-group assignment of 60 novel microsatellite markers for the gray, short-tailed opossum Monodelphis domestica.

    PubMed

    Gouin, Nicolas; Westenberger, Scott J; Mahaney, Susan M; Lindley, Peter; VandeBerg, John L; Samollow, Paul B

    2005-12-01

    Short-tandem-repeat (SSR) or microsatellite polymorphisms are some of the most extensively employed genetic markers in contemporary linkage mapping studies. To date, only a limited number of microsatellites have been isolated in the gray, short-tailed opossum Monodelphis domestica, a South American marsupial widely used for comparative biological and biomedical research. To increase the number of potentially useful mapping markers, we screened 2 microsatellite-enriched genomic libraries containing alternatively (CA)n or (GA)n repeats. A total of 184 clones were sequenced, from which 60 polymorphic microsatellite markers were successfully optimized. The efficiency of this enrichment protocol for M. domestica microsatellite isolation is discussed, and suggestions to improve the outcome are made. All 60 loci showed high allelic diversity, with allele numbers ranging from 2 to 10 in a subset of 33 unrelated animals. Normal Mendelian inheritance was confirmed for all loci by analyzing allelic segregation in 5 two-generation families. One microsatellite appeared to be X linked, and null alleles were found in 5 others. Two-point linkage analyses were implemented using the data on the 5 families, leading to the assignment of 59 of these loci to the existing linkage groups. The 60 novel microsatellites developed in this study will contribute significantly to the M. domestica linkage map, and further QTL mapping studies.

  8. Nonradioactive sequence-tagged microsatellite site analyses: a method transferable to the tropics.

    PubMed

    Lagoda, P J; Dambier, D; Grapin, A; Baurens, F C; Lanaud, C; Noyer, J L

    1998-02-01

    Utilization of existing isozyme analysis facilities to detect sequence-tagged microsatellite site (STMS) polymorphism or any simple sequence repeat (SSR) variation is described. Different parameters concerning the difficulties in transferring molecular techniques to less sophisticated laboratory infrastructures (i.e. tropical outstations) are discussed (e.g. reproducibility, efficacy, precision). Nonradioactive STMS analysis is bound to foster collaborative research between "biodiversity" and "biotechnology" centers.

  9. Isolation and characterization of 11 tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon).

    PubMed

    Rodrigues, Mónica; Fernandes, Carlos A; Palomares, Francisco; Amorim, Isabel R; Bruford, Michael W; Santos-Reis, Margarida

    2009-07-01

    We report the isolation of 11 polymorphic tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon). In a sample of 27 individuals, we observed between 4 and 7 alleles per locus and their observed and expected heterozygosities ranged from 0.37 to 0.85 and from 0.44 to 0.79, respectively. All genotypic frequencies conformed to Hardy-Weinberg equilibrium expectations and there were no instances of linkage disequilibrium detected between pairs of loci.

  10. Development of Y chromosome intraspecific polymorphic markers in the Felidae.

    PubMed

    Luo, Shu-Jin; Johnson, Warren E; David, Victor A; Menotti-Raymond, Marilyn; Stanyon, Roscoe; Cai, Qing Xiu; Beck, Thomas; Yuhki, Naoya; Pecon-Slattery, Jill; Smith, James L D; O'Brien, Stephen J

    2007-01-01

    Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.

  11. Isolation and characterization of microsatellite loci in Branchiostoma belcheri Gray (Amphioxus).

    PubMed

    Li, Z B; Huang, Y S; Shangguan, J B; Ning, Y F; Yi, Y; Dai, G

    2015-08-28

    Branchiostoma belcheri Gray is a second-class, nationally protected protochordate in China. We developed 10 novel polymorphic sites in B. belcheri, which were examined using a population of 30 wild individuals from Xiamen, China. The polymorphism information content ranged between 0.141 and 0.681, and the number of alleles varied from 2 to 5. The expected and observed heterozygosities varied between 0.1528 and 0.6920, and between 0.1429 and 0.5000, respectively. These novel microsatellite markers will facilitate the genetic analysis and protection of wild B. belcheri individuals, and the possible re-stocking of the species in the long-term.

  12. Characterization of new microsatellite markers derived from sequence databases for the emu (Dromaius novaehollandiae).

    PubMed

    Yáñez, José M; González, Ruth; Angulo, Jenniffer; Vidal, Rodrigo; Santos, José L; Martínez, Victor

    2008-11-01

    The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different populations kept in captivity. Between two and 11 alleles were found per locus, and the observed heterozygosity ranged from 0.05 to 0.85, in accordance with expectations. These markers will be useful as tools for detecting levels of genetic variation, reconstructing pedigrees (for quantitative genetic analysis) and identifying markers associated to fitness traits in emu populations.

  13. Characterization of 42 microsatellite markers from poison ivy, Toxicodendron radicans (Anacardiaceae).

    PubMed

    Hsu, Tsai-Wen; Shih, Huei-Chuan; Kuo, Chia-Chi; Chiang, Tzen-Yuh; Chiang, Yu-Chung

    2013-10-14

    Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a species distributed from North America to East Asia, while T. diversilobum and T. pubescens are distributed in western and eastern North America, respectively. Phylogreography and population structure of these species remain unclear. Here, we developed microsatellite markers, via constructing a magnetic enriched microsatellite library, from poison ivy. We designed 51 primer pairs, 42 of which successfully yielded products that were subsequently tested for polymorphism in poison oak, and three subspecies of poison ivy. Among the 42 loci, 38 are polymorphic, while 4 are monomorphic. The number of alleles and the expected heterozygosity ranged from 1 to 12 and from 0.10 to 0.87, respectively, in poison ivy, while varied from 2 to 8 and, from 0.26 to 0.83, respectively in poison oak. Genetic analysis revealed distinct differentiation between poison ivy and poison oak, whereas slight genetic differentiation was detected among three subspecies of poison ivy. These highly polymorphic microsatellite fingerprints enable biologists to explore the population genetics, phylogeography, and speciation in Toxicodendron.

  14. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

    PubMed Central

    Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

    2015-01-01

    Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

  15. Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

    PubMed

    Cai, Guohong; Leadbetter, Clayton W; Muehlbauer, Megan F; Molnar, Thomas J; Hillman, Bradley I

    2013-01-01

    High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps), with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%). After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6%) were successfully amplified and 214 (90.7%) produced single PCR products. Twenty-three (9.7%) were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins. Thus, the

  16. Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES).

    PubMed

    Klein, Akos; Horsburgh, Gavin J; Küpper, Clemens; Major, Agnes; Lee, Patricia L M; Hoffmann, Gyula; Mátics, Róbert; Dawson, Deborah A

    2009-11-01

    We have identified 15 polymorphic microsatellite loci for the barn owl (Tyto alba), five from testing published owl loci and 10 from testing non-owl loci, including loci known to be of high utility in passerines and shorebirds. All 15 loci were sequenced in barn owl, and new primer sets were designed for eight loci. The 15 polymorphic loci displayed two to 26 alleles in 56-58 barn owls. When tested in 10 other owl species (n = 1-6 individuals), between four and nine loci were polymorphic per species. These loci are suitable for studies of population structure and parentage in owls.

  17. Microsatellites in the tree Foetidia mauritiana (Lecythidaceae) and utility in other Foetidia taxa from the Mascarene Islands1

    PubMed Central

    Martos, Florent; Lebreton, Gérard; Rivière, Eric; Humeau, Laurence; Chevallier, Marie-Hélène

    2016-01-01

    Premise of the study: Polymorphic markers were required for a native tree of the Mascarene Islands, Foetidia mauritiana (Lecythidaceae), to investigate the effects of fragmentation of lowland tropical habitats on tree mating systems and on gene flow. Methods and Results: Using microsatellite enrichment and next-generation sequencing, we identified 13 microsatellite loci (dinucleotide repeats). They were highly polymorphic in 121 trees sampled in the largest three populations on Réunion, revealing 2–17 different alleles per locus. Furthermore, they were found to be polymorphic in conspecific populations on Mauritius and in F. rodriguesiana from Rodrigues. Conclusions: These results indicate the utility of these markers to investigate genetic diversity, mating systems, and gene flow in a genus native to the biodiversity hotspot of Madagascar and the Indian Ocean islands. PMID:27610278

  18. Microsatellite primers in Agave utahensis (Asparagaceae), a keystone species in the Mojave Desert and Colorado Plateau1

    PubMed Central

    Byers, Charlee; Maughan, Peter J.; Clouse, Jared; Stewart, J. Ryan

    2014-01-01

    • Premise of the study: Utah agave (Agave utahensis) and its putative subspecies, A. utahensis subsp. kaibabensis and A. utahensis subsp. utahensis, are keystone species of the Mojave Desert and Colorado Plateau in the southwestern United States. Here we developed microsatellite markers to study population structure and genetic diversity of the two subspecies of A. utahensis. • Methods and Results: We analyzed 22,386 454-pyrosequencing large contigs (>400 bp), derived from a genome reduction experiment consisting of A. utahensis accessions, for putative microsatellites. The use of unique multiplex barcodes for each of the Agave accessions allowed for the identification of putatively polymorphic microsatellites based solely on sequence alignment analysis. We report the characteristics of 11 polymorphic microsatellite loci based on a panel of 104 individuals from the two subspecies. The number of alleles per locus varied from three to eight, with an average of 5.5 alleles per locus. Observed and expected heterozygosity values ranged from 0.038 to 0.777 and 0.038 to 0.707, respectively. • Conclusions: The microsatellites identified here will be invaluable for future studies of population structure, polyploidy, and genetic diversity across the species. PMID:25225631

  19. Transferability and utility of white oat (Avena sativa) microsatellite markers for genetic studies in black oat (Avena strigosa).

    PubMed

    Da-Silva, P R; Milach, S C K; Tisian, L M

    2011-11-29

    Preservation and use of wild oat species germplasm are essential for further improvement of cultivated oats. We analyzed the transferability and utility of cultivated (white) oat Avena sativa (AACCDD genome) microsatellite markers for genetic studies of black oat A. strigosa (A(s)A(s) genome) genotypes. The DNA of each black oat genotype was extracted from young leaves and amplified by PCR using 24 microsatellite primers developed from white oat. The PCR products were separated on 3% agarose gel. Eighteen microsatellite primer pairs amplified consistent products and 15 of these were polymorphic in A. strigosa, demonstrating a high degree of transferability. Microsatellite primer pairs AM3, AM4, AM21, AM23, AM30, and AM35 consistently amplified alleles only in A. sativa, which indicates that they are putative loci for either the C or D genomes of Avena. Using the data generated by the 15 polymorphic primer pairs, it was possible to separate 40 genotypes of the 44 that we studied. The four genotypes that could not be separated are probably replicates. We conclude that A. sativa microsatellites have a high transferability index and are a valuable resource for genetic studies and characterization of A. strigosa genotypes.

  20. Microsatellite primers for red drum (Sciaenops ocellatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this note, we document polymerase-chain-reaction (PCR) primer pairs for 101, nuclear-encoded microsatellites designed and developed from a red drum (Sciaenops ocellatus) genomic library. The 101 microsatellites (Genbank Accession Numbers EU015882-EU015982) were amplified successfully and used to...

  1. Sequence determinants of human microsatellite variability

    PubMed Central

    2009-01-01

    Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability. PMID:20015383

  2. Regulation of murine megakaryocyte size and ploidy by non-platelet-dependent mechanisms in radiation-induced megakaryocytopenia

    SciTech Connect

    Ebbe, S. )

    1991-09-01

    Megakaryocytic macrocytosis was evaluated in mice after irradiation with 6.5 Gy 60Co gamma rays. During the second and third months after sublethal irradiation, one or more of the following abnormalities of thrombocytopoiesis was present: thrombocytopenia, megakaryocytopenia, macromegakaryocytosis, a shift to higher ploidies, and enlargement of cells within ploidy groups. After transfusion-induced thrombocytosis, reductions in megakaryocyte size were delayed or absent relative to non-irradiated mice, and there was more of a tendency to shift to lower values for megakaryocyte ploidy. Mice with radiation-induced megakaryocytopenia failed to show rebound thrombocytosis during recovery from immunothrombocytopenia, in spite of further increases in megakaryocyte size and ploidy. The findings support the hypotheses that numbers of megakaryocytes may influence the regulation of megakaryocytopoiesis even when there is an excess of platelets and that ploidy distribution is not the sole determinant of the average size of a population of megakaryocytes. After irradiation, persistent megakaryocytopenia may not severely affect platelet production under steady-state conditions, but the ability of the marrow to respond to homeostatic regulation is compromised.

  3. Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae

    USGS Publications Warehouse

    Moyer, G.R.; Sloss, Brian L.; Kreiser, B.R.; Feldheim, K.A.

    2009-01-01

    We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management. ?? 2009 Blackwell Publishing Ltd.

  4. An improved technique for isolating codominant compound microsatellite markers.

    PubMed

    Lian, Chunlan L; Abdul Wadud, Md; Geng, Qifang; Shimatani, Kenichiro; Hogetsu, Taizo

    2006-07-01

    An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.

  5. Infrequent microsatellite instability in oesophageal cancers.

    PubMed Central

    Muzeau, F.; Fléjou, J. F.; Belghiti, J.; Thomas, G.; Hamelin, R.

    1997-01-01

    Alterations of microsatellites have been found at relatively high frequency in hereditary and sporadic colorectal cancer and gastric and pancreatic cancers and at lower frequency in some other cancers. We determined the frequency of instability at 39 poly-CA microsatellite loci in 20 squamous cell carcinomas and 26 Barrett's adenocarcinomas of the oesophagus. None of the tumours presented instability for a high percentage of the tested loci. Four squamous cell carcinomas and six Barrett's adenocarcinomas showed microsatellite instability at one locus, and three Barrett's adenocarcinomas showed microsatellite instability at two loci. The presence of few loci showing microsatellite instability could be due to an instability background. We conclude that genetic defects in the DNA mismatch repair system do not play an important role in oesophageal cancers. Images Figure 1 PMID:9155055

  6. Cross-amplification and characterization of microsatellite loci in Acropora austera from the south-western Indian Ocean.

    PubMed

    Montoya-Maya, P H; Macdonald, A H H; Schleyer, M H

    2014-02-27

    Here, we report the successful cross-species amplification of previously published acroporid microsatellite markers in the coral Acropora austera from the south-western Indian Ocean. This fast-growing species is a major reef-building coral on South African reefs; however, it is the most damaged coral by scuba diving activity, and is known to be very susceptible to coral bleaching. Neither genetic information nor symbiont-free host tissue was available to develop novel microsatellite markers for this species. Cross-species amplification of previously published microsatellite markers was considered as an alternative to overcome these problems. Of the 21 microsatellite markers tested, 6 were reliably amplified, scored, and found to contain polymorphic loci (3-15 alleles). Although microsatellite sequences are believed to be scarce in the Acropora genome because of its small size, the results of this study and previous research indicate that the microsatellite sequences are well conserved across Acropora species. A detailed screening process identified and quantified the sources of error and bias in the application of these markers (e.g., allele scoring error, failure rates, frequency of null alleles), and may be accounted for in the study of the contemporary gene flow of A. austera in the south-western Indian Ocean.

  7. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century1

    PubMed Central

    Hodel, Richard G. J.; Segovia-Salcedo, M. Claudia; Landis, Jacob B.; Crowl, Andrew A.; Sun, Miao; Liu, Xiaoxian; Gitzendanner, Matthew A.; Douglas, Norman A.; Germain-Aubrey, Charlotte C.; Chen, Shichao; Soltis, Douglas E.; Soltis, Pamela S.

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. PMID:27347456

  8. Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).

    PubMed

    Song, Xuhao; Shen, Fujun; Huang, Jie; Huang, Yan; Du, Lianming; Wang, Chengdong; Fan, Zhenxin; Hou, Rong; Yue, Bisong; Zhang, Xiuyue

    2016-09-01

    Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.

  9. Hybridization between two cryptic filamentous brown seaweeds along the shore: Analysing pre- and post-zygotic barriers in populations of individuals with varying ploidy levels.

    PubMed

    Montecinos, Alejandro E; Guillemin, Marie-Laure; Couceiro, Lucia; Peters, Akira F; Stoeckel, Solenn; Valero, Myriam

    2017-03-12

    We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly post-zygotic and suggests that abnormal chromosome segregation during meiosis following hybridisation of species with different genome sizes could be a major cause of interspecific incompatibility in this system. This article is protected by copyright. All rights reserved.

  10. A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags.

    PubMed

    Tani, Naoki; Takahashi, Tomokazu; Iwata, Hiroyoshi; Mukai, Yuzuru; Ujino-Ihara, Tokuko; Matsumoto, Asako; Yoshimura, Kensuke; Yoshimaru, Hiroshi; Murai, Masafumi; Nagasaka, Kazutoshi; Tsumura, Yoshihiko

    2003-11-01

    A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

  11. Ploidy of cell-sorted trophic and cystic forms of Pneumocystis carinii.

    PubMed

    Martinez, Anna; Aliouat, El Moukhtar; Standaert-Vitse, Annie; Werkmeister, Elisabeth; Pottier, Muriel; Pinçon, Claire; Dei-Cas, Eduardo; Aliouat-Denis, Cécile-Marie

    2011-01-01

    Once regarded as an AIDS-defining illness, Pneumocystis pneumonia (PcP) is nowadays prevailing in immunocompromised HIV-negative individuals such as patients receiving immunosuppressive therapies or affected by primary immunodeficiency. Moreover, Pneumocystis clinical spectrum is broadening to non-severely-immunocompromised subjects who could be colonized by the fungus while remaining asymptomatic for PcP, thus being able to transmit the infection by airborne route to susceptible hosts. Although the taxonomical position of the Pneumocystis genus has been clarified, several aspects of its life cycle remain elusive such as its mode of proliferation within the alveolus or its ploidy level. As no long-term culture model exists to grow Pneumocystis organisms in vitro, an option was to use a model of immunosuppressed rat infected with Pneumocystis carinii and sort life cycle stage fractions using a high-through-put cytometer. Subsequently, ploidy levels of the P. carinii trophic and cystic form fractions were measured by flow cytometry. In the cystic form, eight contents of DNA were measured thus strengthening the fact that each mature cyst contains eight haploid spores. Following release, each spore evolves into a trophic form. The majority of the trophic form fraction was haploid in our study. Some less abundant trophic forms displayed two contents of DNA indicating that they could undergo (i) mating/fusion leading to a diploid status or (ii) asexual mitotic division or (iii) both. Even less abundant trophic forms with four contents of DNA were suggestive of mitotic divisions occurring following mating in diploid trophic forms. Of interest, was the presence of trophic forms with three contents of DNA, an unusual finding that could be related to asymmetrical mitotic divisions occurring in other fungal species to create genetic diversity at lower energetic expenses than mating. Overall, ploidy data of P. carinii life cycle stages shed new light on the complexity of its

  12. Ploidy of Cell-Sorted Trophic and Cystic Forms of Pneumocystis carinii

    PubMed Central

    Martinez, Anna; Aliouat, El Moukhtar; Standaert-Vitse, Annie; Werkmeister, Elisabeth; Pottier, Muriel; Pinçon, Claire; Dei-Cas, Eduardo; Aliouat-Denis, Cécile-Marie

    2011-01-01

    Once regarded as an AIDS-defining illness, Pneumocystis pneumonia (PcP) is nowadays prevailing in immunocompromised HIV-negative individuals such as patients receiving immunosuppressive therapies or affected by primary immunodeficiency. Moreover, Pneumocystis clinical spectrum is broadening to non-severely-immunocompromised subjects who could be colonized by the fungus while remaining asymptomatic for PcP, thus being able to transmit the infection by airborne route to susceptible hosts. Although the taxonomical position of the Pneumocystis genus has been clarified, several aspects of its life cycle remain elusive such as its mode of proliferation within the alveolus or its ploidy level. As no long-term culture model exists to grow Pneumocystis organisms in vitro, an option was to use a model of immunosuppressed rat infected with Pneumocystis carinii and sort life cycle stage fractions using a high-through-put cytometer. Subsequently, ploidy levels of the P. carinii trophic and cystic form fractions were measured by flow cytometry. In the cystic form, eight contents of DNA were measured thus strengthening the fact that each mature cyst contains eight haploid spores. Following release, each spore evolves into a trophic form. The majority of the trophic form fraction was haploid in our study. Some less abundant trophic forms displayed two contents of DNA indicating that they could undergo (i) mating/fusion leading to a diploid status or (ii) asexual mitotic division or (iii) both. Even less abundant trophic forms with four contents of DNA were suggestive of mitotic divisions occurring following mating in diploid trophic forms. Of interest, was the presence of trophic forms with three contents of DNA, an unusual finding that could be related to asymmetrical mitotic divisions occurring in other fungal species to create genetic diversity at lower energetic expenses than mating. Overall, ploidy data of P. carinii life cycle stages shed new light on the complexity of its

  13. Ploidy race distributions since the Last Glacial Maximum in the North American desert shrub, Larrea tridentata

    USGS Publications Warehouse

    Hunter, K.L.; Betancourt, J.L.; Riddle, B.R.; Van Devender, T. R.; Cole, K.L.; Geoffrey, Spaulding W.

    2000-01-01

    1 A classic biogeographic pattern is the alignment of diploid, tetraploid and hexaploid races of creosote bush (Larrea tridentata) across the Chihuahuan, Sonoran and Mohave Deserts of western North America. We used statistically robust differences in guard cell size of modern plants and fossil leaves from packrat middens to map current and past distributions of these ploidy races since the Last Glacial Maximum (LGM). 2 Glacial/early Holocene (26-10 14C kyr BP or thousands of radiocarbon years before present) populations included diploids along the lower Rio Grande of west Texas, 650 km removed from sympatric diploids and tetraploids in the lower Colorado River Basin of south-eastern California/south-western Arizona. Diploids migrated slowly from lower Rio Grande refugia with expansion into the northern Chihuahuan Desert sites forestalled until after ???4.0 14C kyr BP. Tetraploids expanded from the lower Colorado River Basin into the northern limits of the Sonoran Desert in central Arizona by 6.4 14C kyr BP. Hexaploids appeared by 8.5 14C kyr BP in the lower Colorado River Basin, reaching their northernmost limits (???37??N) in the Mohave Desert between 5.6 and 3.9 14C kyr BP. 3 Modern diploid isolates may have resulted from both vicariant and dispersal events. In central Baja California and the lower Colorado River Basin, modern diploids probably originated from relict populations near glacial refugia. Founder events in the middle and late Holocene established diploid outposts on isolated limestone outcrops in areas of central and southern Arizona dominated by tetraploid populations. 4 Geographic alignment of the three ploidy races along the modern gradient of increasingly drier and hotter summers is clearly a postglacial phenomenon, but evolution of both higher ploidy races must have happened before the Holocene. The exact timing and mechanism of polyploidy evolution in creosote bush remains a matter of conjecture. ?? 2001 Blackwell Science Ltd.

  14. Ploidy race distributions since the Last Glacial Maximum in the North American desert shrub, Larea tridentata

    USGS Publications Warehouse

    Hunter, Kimberly L.; Betancourt, Julio L.; Riddle, Brett R.; Van Devender, Thomas R.; Cole, K.L.; Spaulding, W.G.

    2001-01-01

    1. A classic biogeographic pattern is the alignment of diploid, tetraploid and hexaploid races of creosote bush (Larrea tridentata) across the Chihuahuan, Sonoran and Mohave Deserts of western North America. We used statistically robust differences in guard cell size of modern plants and fossil leaves from packrat middens to map current and past distributions of these ploidy races since the Last Glacial Maximum (LGM). 2 Glacial/early Holocene (26a??10 14C kyr bp or thousands of radiocarbon years before present) populations included diploids along the lower Rio Grande of west Texas, 650 km removed from sympatric diploids and tetraploids in the lower Colorado River Basin of south-eastern California/south-western Arizona. Diploids migrated slowly from lower Rio Grande refugia with expansion into the northern Chihuahuan Desert sites forestalled until after ~4.0 14C kyr bp. Tetraploids expanded from the lower Colorado River Basin into the northern limits of the Sonoran Desert in central Arizona by 6.4 14C kyr bp. Hexaploids appeared by 8.5 14C kyr bp in the lower Colorado River Basin, reaching their northernmost limits (~37A?N) in the Mohave Desert between 5.6 and 3.9 14C kyr bp. 3 Modern diploid isolates may have resulted from both vicariant and dispersal events. In central Baja California and the lower Colorado River Basin, modern diploids probably originated from relict populations near glacial refugia. Founder events in the middle and late Holocene established diploid outposts on isolated limestone outcrops in areas of central and southern Arizona dominated by tetraploid populations. 4 Geographic alignment of the three ploidy races along the modern gradient of increasingly drier and hotter summers is clearly a postglacial phenomenon, but evolution of both higher ploidy races must have happened before the Holocene. The exact timing and mechanism of polyploidy evolution in creosote bush remains a matter of conjecture.

  15. A simplified molecular method for distinguishing among species and ploidy levels in European water frogs (Pelophylax).

    PubMed

    Hauswaldt, J Susanne; Höer, Manuela; Ogielska, Maria; Christiansen, Ditte G; Dziewulska-Szwajkowska, Daria; Czernicka, Elżbieta; Vences, Miguel

    2012-09-01

    Western Palearctic water frogs in the genus Pelophylax are a set of morphologically similar anuran species that form hybridogenetic complexes. Fully reliable identification of species and especially of hybrid ploidy depends on karyological and molecular methods. In central Europe, native water frog populations consist of the Pelophylax esculentus complex, that is, P. lessonae (LL), P. ridibundus (RR) and the hybrid form P. esculentus that can have different karyotypes (RL, LLR and RRL). We developed existing molecular methods further and propose a simple PCR method based on size-differences in the length of the serum albumin intron-1 and the RanaCR1, a non-LTR retrotransposon of the chicken repeat (CR) family. This PCR yields taxon-specific banding patterns that can easily be screened by standard agarose gel electrophoresis and correctly identify species in all of the 160 samples that had been identified to karyotype with other methods. To distinguish ploidy levels in LR, LLR and RRL specimens, we used the ratio of the peak heights of the larger (ridibundus specific) to the smaller (lessonae specific) bands of fluorescently labelled PCR products resolved on a capillary DNA sequencer and obtained a correct assignment of the karyotype in 93% of cases. Our new method will cut down time and expenses drastically for a reliable identification of water frogs of the P. esculentus complex and potentially for identification of other hybridogenetic complexes and/or taxa, and it even serves as a good indicator of the ploidy status of hybrid individuals.

  16. Gene expression in diplosporous and sexual Eragrostis curvula genotypes with differing ploidy levels.

    PubMed

    Cervigni, Gerardo D L; Paniego, Norma; Pessino, Silvina; Selva, Juan P; Díaz, Marina; Spangenberg, Germán; Echenique, Viviana

    2008-05-01

    The molecular nature of gene expression during the initiation and progress of diplosporous apomixis is still unknown. Moreover, the basis of the close correlation between diplospory and polyploidy is not clarified yet. A comparative expression analysis was performed based on expressed sequence tags (ESTs) sequencing and differential display in an Eragrostis curvula diplosporous tetraploid genotype (T, 4x apo), a sexual diploid derivative obtained from tissue culture (D, 2x sex) and an artificial sexual tetraploid obtained from the diploid seeds after colchicine treatment (C, 4x sex). From a total of 8,884 unigenes sequenced from inflorescence-derived libraries, 112 (1.26%) showed significant differential expression in individuals with different ploidy level and/or variable reproductive mode. Independent comparisons between plants with different reproductive mode (same ploidy) or different ploidy level (same reproductive mode) allowed the identification of genes modulated in response to diplosporous development or polyploidization, respectively. Surprisingly, a group of genes (Group 3) were differentially expressed or silenced only in the 4x sex plant, presenting similar levels of expression in the 4x apo and the 2x sex genotypes. A group of randomly selected differential genes was validated by QR-PCR. Differential display analysis showed that in general the 4x apo and 4x sex expression profiles were more related and different from the 2x sex one, but confirmed the existence of Group 3-type genes, in both inflorescences and leaves. The possible biological significance for the occurrence of this particular group of genes is discussed. In silico mapping onto the rice genome was used to identify candidates mapping to the region syntenic to the diplospory locus.

  17. [Differentiation of chum salmon Oncorhynchus keta Walbaum populations as revealed with microsatellite and allozyme markers: a comparison].

    PubMed

    Rubtsoba, G A; Afanas'ev, K I; Malinina, T V; Shitova, M V; Rakitskaia, T A; Prokhorovskaia, V D; Zhivotovskiĭ, L A

    2008-07-01

    The character and extent of population differentiation in chum salmon Oncorhynchus keta from Sakhalin and Iturup were comparatively studied with 10 microsatellite and 12 allozyme markers. It was demonstrated with the example of allozyme polymorphism at the EstD locus that the effect of an individual locus with one major allele is capable of distorting the total picture of population differentiation. Multiallelic microsatellites were more efficient in revealing the genetic structure of chum salmon populations at the levels of differences between regional populations and between the stocks of individual rivers of the same region.

  18. Ploidy pattern of megakaryocytes in patients with metastatic tumors with and without paraneoplastic thrombosis and in controls.

    PubMed

    Winkelmann, M; Stöckler, J; Grassmuck, J; Pfitzer, P; Schneider, W

    1984-01-01

    In order to measure megakaryocyte DNA content in a greater number of well-defined patients, the use of bone marrow aspirates obtained postmortem is a basic requirement. We could show that the distinction between the ploidy classes in DNA histograms is possible until 18 h postmortem. Thus, bone marrow aspirates obtained up to 12 h after death can be expected to give reliable results. Megakaryocytes of the following patient groups were studied: 15 patients with metastatic tumors and paraneoplastic thrombosis, 15 patients with metastatic tumors without paraneoplastic thrombosis and 10 controls. A higher ploidy of the megakaryocytes was found in all 30 patients with metastatic tumors, independently of whether these patients suffer from thrombosis or not. Higher megakaryocyte ploidy, however, is correlated with a larger cytoplasmic mass of megakaryocytes, which leads to an increased platelet production. Besides an overcompensation for increased platelet consumption, a mitogenic or thrombopoietin-like factor produced by the tumor itself must be considered.

  19. Microsatellite markers for the yam bean Pachyrhizus (Fabaceae)1

    PubMed Central

    Delêtre, Marc; Soengas, Beatriz; Utge, José; Lambourdière, Josie; Sørensen, Marten

    2013-01-01

    • Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. • Methods and Results: Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. • Conclusions: By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus. PMID:25202568

  20. Microsatellite primers for the rare sedge Lepidosperma bungalbin (Cyperaceae)1

    PubMed Central

    Nevill, Paul G.; Wardell-Johnson, Grant

    2016-01-01

    Premise of the study: Microsatellite markers were developed for the rare sedge Lepidosperma bungalbin (Cyperaceae) to assess genetic variation and its spatial structuring. Methods and Results: We conducted shotgun sequencing on an Illumina MiSeq and produced 6,215,872 sequence reads. The QDD pipeline was used to design 60 primer pairs that were screened using PCR. We developed 17 loci, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored. We then screened these loci for variation in individuals from three populations. The number of alleles observed for these 12 loci across the three populations ranged from nine to 19 and expected heterozygosity ranged from 0.41 to 0.89. Conclusions: These markers will enable the quantification of the potential impact of mining on genetic variation within L. bungalbin and establish a baseline for future management of genetic variation of the rare sedge. PMID:27843727

  1. Microsatellite primers for the rare shrub Acacia adinophylla (Fabaceae)1

    PubMed Central

    Nevill, Paul G.; Wardell-Johnson, Grant

    2016-01-01

    Premise of the study: Microsatellite primers were developed for the rare shrub Acacia adinophylla (Fabaceae) to assess genetic diversity and its spatial structuring. Methods and Results: Shotgun sequencing on an Illumina MiSeq produced 6,372,575 reads. Using the QDD pipeline, we designed 60 primer pairs, which were screened using PCR. Seventeen loci were developed, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored. These loci were then screened for variation in individuals from three populations. The number of alleles observed for these 12 loci ranged from three to 18 and expected heterozygosity ranged from 0.13 to 0.85. Conclusions: These markers will enable the quantification of genetic impact of proposed mining activities on the short-range endemic Acacia adinophylla. PMID:27843728

  2. Microsatellite variation in red-winged blackbirds (Agelaius phoeniceus).

    PubMed

    Williams, C Lenney; Homan, H J; Johnston, J J; Linz, G M

    2004-02-01

    Territorial male red-winged blackbirds from five locations in the United States and Canada were genotyped using a suite of six microsatellite loci. Each population possessed unique alleles, but numbers of alleles per locus (range = 7.3-8.8) and expected multilocus heterozygosities (range = 0.76-0.80) were similar in all populations. Significant overall allele frequency differences were detected between some population pairs, and some pairwise Fst values were significant (but small). However, Fst among populations, although significant, was also small (0.009). Despite revealing low levels of population structure, the high multilocus polymorphism indicates these loci will be valuable in the genetic analysis of behavior and reproductive strategies in this species.

  3. Development of an affordable typing method for Meyerozyma guilliermondii using microsatellite markers.

    PubMed

    Wrent, Petra; Rivas, Eva-María; Peinado, José M; de Silóniz, María-Isabel

    2016-01-18

    Despite previously published methods, there is still a lack of rapid and affordable methods for genotyping the Meyerozyma guilliermondii yeast species. The development of microsatellite markers is a useful genotyping method in several yeast species. Using the Tandem Repeat Finder Software, a total of 19 microsatellite motifs (di-, tri-, and tetra- repetition) were found in silico in seven of the nine scaffolds published so far. Primer pairs were designed for all of them, although only four were used in this work. All microsatellite amplifications showed size polymorphism, and the results were identical when repeated. The combination of three microsatellite markers (sc15F/R, sc32 F/R and sc72 F/R) produced a different pattern for each of the Type Culture Collection strains of M. guilliermondii used to optimize the method. The three primer pairs can be used in the same PCR reaction, which reduces costs, in tandem with the fluorescent labeling of only the forward primer in each primer pair. Microsatellite typing was applied on 40 more M. guilliermondii strains. The results showed that no pattern is repeated between the different environmental niches. Four M. guilliermondii strains were only amplified with primer pair sc32 F/R, and subsequently identified as Meyerozyma caribbica by Taq I-RFLP of the 5.8S ITS rDNA. Most out-group species gave negative results even for physiologically similarly species such as Debaryomyces hansenii. The microsatellite markers used in this work were stable over time, which enables their use as a traceability tool.

  4. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

    PubMed

    Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

  5. Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single-nucleotide polymorphisms (SNPs) are the most common genetic markers in Theobroma cacao, occurring approximately once in every 200 nucleotides. SNPs, like microsatellites, are co-dominant and PCR-based, but they have several advantages over microsatellites. They are unambiguous, so that a SN...

  6. Passive cryocooler for microsatellite payload

    NASA Astrophysics Data System (ADS)

    Mullins, Mayes; Thomas, Paul J.; Harron, John W.; Duggan, Philip; Sinclair, Peter M.; Khanna, Shyam M.

    1998-11-01

    A passive cryocooler has been developed for the cooling of small payloads to temperatures as low as 145 K. Although designed for a specific electronics experiment on the STRV-1d microsatellite, the device is suitable for a wide range of applications. The cryocooler uses coated surfaces for tailored radiative cooling. Mechanical support between components is provided by fiberglass struts. The measured end temperature reached is 151 K in a liquid nitrogen dewar which extrapolates to an end temperature of lower than 145 K in space. Thermal vacuum testing and random vibration testing at levels consistent with an Ariane 5 launch have been performed as part of formal qualification for the STRV mission. In this paper, details of the design, analysis, fabrication and testing of the passive cryocooler are presented.

  7. Microsatellite instability in prostate cancer

    SciTech Connect

    Shan, A.L.; Wick, M.J.; Persons, D.L.

    1994-09-01

    Microsatellite instability (MIN) has been documented in hereditary nonpolyposis colorectal cancer (HNPCC) as well as in sporadic forms of human cancers. Two of the genes which appear to be responsible for this particular tumor phenotype, hMSH2 and hMLH1, have now been identified. To determine the potential role of these mutator genes in prostate cancer, we have examined 95 prostate adenocarcinomas (40 paraffin embedded and 55 fresh frozen) for the presence of genetic instability at four microsatellite markers. The markers are localized to chromosome arms 5q(APC-CA1), 8p(Mfd 210Z), 15q(635/636), and 17q(p53-CA). Patients from whom paraffin embedded material was obtained were divided into short term (<3 years, n=18), and long term (>3 years, n=22) survivors. Of the 95 tumors examined, only four tumors (4%) demonstrated MIN: two tumors demonstrated MIN at 3 loci (p53-CA, APC-CA1, 635/636), one tumor demonstrated MIN at 2 loci (APC-CA1 and 635/636), and one tumor demonstrated instability at 635/636 only. All tumors exhibiting MIN had Gleason scores of {ge} 4+4. A correlation between MIN and survival was not observed. Information on family history was limited. However, of the two patients demonstrating MIN at three loci, one patient was diagnosed with a second malignancy (TCC of the ureter), but otherwise had a negative family history, while the second patient had one first degree relative with esophageal cancer. The patient demonstrating MIN at two loci had a negative family history, while the remaining patient had two first degree relatives with cancer (prostate and stomach). These results suggest that hMSH2 and hMLH1 (as reflected by the small percentage of tumors displaying MIN) do not play a prominent role in the process of prostate tumorigenesis.

  8. Survey of compound microsatellites in multiple Lactobacillus genomes.

    PubMed

    Basharat, Zarrin; Yasmin, Azra

    2015-12-01

    Distinct simple sequence repeats with 2 or more individual microsatellites joined together or lying adjacent to each other are identified as compound microsatellites. Investigation of such composite microsatellites in the genomes of genus Lactobacillus was the aim of this study. In silico inspection of microsatellite clustering in genomes of 14 Lactobacillus species revealed a wealth of compound microsatellites. All of the mined compound microsatellites were imperfect, were composed of variant motifs, and increased in all genomes, with maximum distance (dMAX) increments of 10 to 50. The majority of these repeats were present in the coding regions. A correlation of microsatellite to compound microsatellite density was detected. The difference established in compound microsatellite division among eukaryotes, Escherichia coli, and lactobacilli is suggestive of diverse genomic features and elementary distinction between creation and fixation methods of compound microsatellites among these organisms.

  9. Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China.

    PubMed

    Du, X Y; Yi, S; Huo, X Y; Wang, C; Liu, D F; Ren, W Z; Chen, Z W

    2015-03-13

    We optimized a panel of microsatellite markers from cat and tiger genetic data for efficient genetic monitoring and used it to analyze the genetic structure of an outbred cat stock in China. We selected a set of rich polymorphic microsatellite loci from 131 cat microsatellite loci and 3 Sumatran tiger microsatellite loci using agarose gel electrophoresis. Next, the set of optimized genetic markers was used to analyze the genetic variation in an outbred population of orange tabby cats in China by simple-tandem repeat scanning. Thirty-one loci rich in polymorphisms were selected and the highest allele number in a single locus was 8. Analysis of the orange tabby cat population illustrated that the average observed number of alleles, mean effective allele number, mean Shannon's information index, mean expected heterozygosity, and observed heterozygosity were 3.8387, 2.4027, 0.9787, 0.5565, and 0.5528, respectively. The 31 microsatellite markers used were polymorphic and suitable for analyzing the genetic structure of cats. The population of orange tabby cats was confirmed to be a well-outbred stock.

  10. Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers.

    PubMed

    Abdul Muneer, P M; Gopalakrishnan, A; Musammilu, K K; Mohindra, Vindhya; Lal, K K; Basheer, V S; Lakra, W S

    2009-09-01

    Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.

  11. Comparative Population Dynamics of Two Closely Related Species Differing in Ploidy Level

    PubMed Central

    Černá, Lucie; Münzbergová, Zuzana

    2013-01-01

    Background Many studies compare the population dynamics of single species within multiple habitat types, while much less is known about the differences in population dynamics in closely related species in the same habitat. Additionally, comparisons of the effect of habitat types and species are largely missing. Methodology and Principal Findings We estimated the importance of the habitat type and species for population dynamics of plants. Specifically, we compared the dynamics of two closely related species, the allotetraploid species Anthericum liliago and the diploid species Anthericum ramosum, occurring in the same habitat type. We also compared the dynamics of A. ramosum in two contrasting habitats. We examined three populations per species and habitat type. The results showed that single life history traits as well as the mean population dynamics of A. liliago and A. ramosum from the same habitat type were more similar than the population dynamics of A. ramosum from the two contrasting habitats. Conclusions Our findings suggest that when transferring knowledge regarding population dynamics between populations, we need to take habitat conditions into account, as these conditions appear to be more important than the species involved (ploidy level). However, the two species differ significantly in their overall population growth rates, indicating that the ploidy level has an effect on species performance. In contrast to what has been suggested by previous studies, we observed a higher population growth rate in the diploid species. This is in agreement with the wider range of habitats occupied by the diploid species. PMID:24116057

  12. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

    PubMed Central

    Zhu, Yuan O.; Sherlock, Gavin; Petrov, Dmitri A.

    2016-01-01

    Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker’s/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in ye